CHRONIC ILLNET REPORT: #8

BACK

Alu retroelements comprise about 5% of the human genome. The name is derived from their property of being cut by the restriction enzyme from Arthrobacter luteus (Alu). Alu retroelements are part of the family of jumping genes known as short interspersed elements or SINEs. Alus are roughly 300 nucleotides in length and contain left and right monomers. An RNA polymerase III start site is located in the Alu with the termination codon found in the adjoining flanking region. Alus are expressed as a result of cellular insult and believed to be part of the mechanism of primate evolution. Alus are involved in recombination with other Alus and their flanking region. It would appear that Alus are actively involved in the chronic disease process and the associated medical literature is presented below.

Reading List

Huie, M. L., A. L. Shanske, J. S. Kasper, R. W. Marion, and R. Hirschhorn. 1999. A large Alu-mediated deletion, identified by PCR, as the molecular basis for glycogen storage disease type II (GSDII). Hum Genet. 104(1):94-8.

Glycogen storage disease type II (GSDII) is an autosomal recessive disorder resulting from inherited deficiency of the enzyme lysosomal acid alpha-glucosidase. Over 40 different mutations have been described but no large deletions have been previously identified. We now describe a homozygous large (9-kb) deletion extending from IVS 15 to 4 kb downstream of the terminal exon (exon 20), detected by polymerase chain reaction (PCR)-based methods. The deletion was initially suspected because of failure to amplify a contiguous group of exons by PCR. We hypothesized an Alu/Alu recombination, based on our prior demonstration by Southern blotting of Alu elements in the regions potentially flanking the deletion. Additional sequence analysis of genomic fragments confirmed the presence of Alu elements and allowed the design of flanking primers for PCR amplification. Amplification resulted in a smaller than normal fragment (0.7 vs. 10 kb) in homozygosity in the proband and in heterozygosity in her parents. Cloning and sequencing of the smaller than normal 0.7-kb deletion fragment revealed an Alu/Alu deletion junction. In heterozygosity this deletion would not be detected by currently standard PCR mutation detection methods. Based on other Alu-mediated deletions, this deletion is likely to be recurrent and should be screened for in all non-consanguineous GSDII patients, particularly when only one mutation has been identified and none of the 12 single-nucleotide polymorphisms in the deleted region are heterozygous. These observations also suggest that initial characterization of genes at disease-causing loci should include a search for Alu and other repetitive elements to facilitate subsequent PCR-based mutation analysis.

Luk'yanov, D. V., G. F. Reshetnikova, and O. I. Podgornaya. 1999. Affinity purification of Alu-DNA-repeat-binding proteins from human somatic cells. Biochemistry (Mosc). 64(1):17-24.

A 66-kD Alu-DNA-repeat binding protein was identified in human somatic cell nucleoplasm. Gel shift assay, southwestern blotting, and affinity purification on DNA attached to a carrier were used. A 60-kD protein copurified with the 66-kD protein during affinity purification, probably due to protein--protein interactions. The gel shift assay reveals multiple complexes with exponential dependence of their relative mobility. The short binding site of the 66-kD protein was defined with the help of synthetic oligonucleotides. It is localized between the A and B boxes of RNA polymerase III promotor and is the same as that reported for the Alu-binding protein from human spermatozoids. The same short binding site, the similarity of the isolation procedure from germ and somatic cells, and similar binding properties and molecular masses suggest homology of the two proteins. The relationship of the proteins we studied and the Alu-DNA-binding proteins described in the literature is discussed.

Oldridge, M., E. H. Zackai, D. M. McDonald-McGinn, S. Iseki, G. M. Morriss-Kay, S. R. Twigg, D. Johnson, S. A. Wall, W. Jiang, C. Theda, E. W. Jabs, and A. O. Wilkie. 1999. De novo alu-element insertions in FGFR2 identify a distinct pathological basis for apert syndrome [In Process Citation]. Am J Hum Genet. 64(2):446-61.

Apert syndrome, one of five craniosynostosis syndromes caused by allelic mutations of fibroblast growth-factor receptor 2 (FGFR2), is characterized by symmetrical bony syndactyly of the hands and feet. We have analyzed 260 unrelated patients, all but 2 of whom have missense mutations in exon 7, which affect a dipeptide in the linker region between the second and third immunoglobulin-like domains. Hence, the molecular mechanism of Apert syndrome is exquisitely specific. FGFR2 mutations in the remaining two patients are distinct in position and nature. Surprisingly, each patient harbors an Alu-element insertion of approximately 360 bp, in one case just upstream of exon 9 and in the other case within exon 9 itself. The insertions are likely to be pathological, because they have arisen de novo; in both cases this occurred on the paternal chromosome. FGFR2 is present in alternatively spliced isoforms characterized by either the IIIb (exon 8) or IIIc (exon 9) domains (keratinocyte growth-factor receptor [KGFR] and bacterially expressed kinase, respectively), which are differentially expressed in mouse limbs on embryonic day 13. Splicing of exon 9 was examined in RNA extracted from fibroblasts and keratinocytes from one patient with an Alu insertion and two patients with Pfeiffer syndrome who had nucleotide substitutions of the exon 9 acceptor splice site. Ectopic expression of KGFR in the fibroblast lines correlated with the severity of limb abnormalities. This provides the first genetic evidence that signaling through KGFR causes syndactyly in Apert syndrome.

Puget, N., O. M. Sinilnikova, D. Stoppa-Lyonnet, C. Audoynaud, S. Pages, H. T. Lynch, D. Goldgar, G. M. Lenoir, and S. Mazoyer. 1999. An Alu-mediated 6-kb duplication in the BRCA1 gene: a new founder mutation? [letter]. Am J Hum Genet. 64(1):300-2.

Halling, K. C., C. R. Lazzaro, R. Honchel, J. A. Bufill, S. M. Powell, C. A. Arndt, and N. M. Lindor. 1999. Hereditary desmoid disease in a family with a germline alu I repeat mutation of the APC gene [In Process Citation]. Hum Hered. 49(2):97-102.

Two families with autosomal dominantly inherited desmoid tumors have recently been shown to have germline mutations at the 3' end of the APC gene. We subsequently identified an Amish family with autosomal dominantly inherited desmoid tumors. Genetic analysis performed on one family member, a 47-year-old man with multiple desmoid tumors and no colon polyps, revealed a protein truncating mutation in the middle of the APC gene. The truncating mutation is the result of a 337-bp insertion of an Alu I sequence into codon 1526 of the APC gene. The presence of a poly(A) tail at the 3' end of the insertion suggests that the Alu I sequence was inserted by a retrotranspositional event. Germline insertions of Alu I sequences have occasionally been reported to cause other genetic diseases including type I neurofibromatosis, hereditary site-specific breast cancer (BRCA2), and hemophilia B. However, this is the first report of a germline mutation of the APC gene resulting from an Alu I insertion.

Blinov, V. M., S. M. Resenchuk, D. L. Uvarov, G. B. Chirikova, S. I. Denisov, and L. L. Kiselev. 1998. [Alu elements in human genome. Invariant secondary structure of left and right monomers]. Mol Biol (Mosk). 32(1):84-92.

Chen, Y., K. Sinha, K. Perumal, J. Gu, and R. Reddy. 1998. Accurate 3' end processing and adenylation of human signal recognition particle RNA and alu RNA in vitro. J Biol Chem. 273(52):35023-31.

Human signal recognition particle (SRP) RNA is transcribed by RNA polymerase III and terminates with -GUCUCUUUUOH on its 3' end. Our previous studies showed that the three terminal uridylic acid residues of human SRP RNA are post-transcriptionally removed and a single adenylic acid residue is added, resulting in a 3' end sequence of - GUCUCUAOH (Sinha, K. M., Gu, J., Chen, Y., and Reddy, R. (1998) J. Biol. Chem. 273, 6853-6859). In this study we show that the Alu RNA, corresponding to the 5' and 3' ends of SRP RNA, is also accurately processed and adenylated in vitro. Alu RNAs containing 7 or 11 additional nucleotides on the 3' end were accurately processed and then adenylated. Deletion analysis showed that an 87-nucleotide-long motif comprising of the 5' and 3' ends, including stem IV of the Alu RNA, is sufficient and necessary for the 3' end processing and adenylation. A 73-nucleotide-long construct with deletion of stem IV, required for the binding of SRP 9/14-kDa proteins, was neither processed nor adenylated. The adenylated Alu RNA as well as adenylated SRP RNA were bound to the SRP 9/14-kDa heterodimer and were immunoprecipitated by specific antibodies. A significant fraction of SRP RNA in the nucleoli was found to be processed and adenylated. These data are consistent with nascent SRP and/or Alu RNAs first binding to SRP 9/14-kDa protein heterodimer, followed by the removal of extra sequence on the 3' end and then the addition of one adenylic acid residue in the nucleus, before transport into the cytoplasm.

Chu, W. M., R. Ballard, B. W. Carpick, B. R. Williams, and C. W. Schmid. 1998. Potential Alu function: regulation of the activity of double-stranded RNA-activated kinase PKR. Mol Cell Biol. 18(1):58-68.

Cell stress, viral infection, and translational inhibition increase the abundance of human Alu RNA, suggesting that the level of these transcripts is sensitive to the translational state of the cell. To determine whether Alu RNA functions in translational homeostasis, we investigated its role in the regulation of double-stranded RNA- activated kinase PKR. We found that overexpression of Alu RNA by cotransient transfection increased the expression of a reporter construct, which is consistent with an inhibitory effect on PKR. Alu RNA formed stable, discrete complexes with PKR in vitro, bound PKR in vivo, and antagonized PKR activation both in vitro and in vivo. Alu RNAs produced by either overexpression or exposure of cells to heat shock bound PKR, whereas transiently overexpressed Alu RNA antagonized virus-induced activation of PKR in vivo. Cycloheximide treatment of cells decreased PKR activity, coincident with an increase in Alu RNA. These observations suggest that the increased levels of Alu RNAs caused by cellular exposure to different stresses regulate protein synthesis by antagonizing PKR activation. This provides a functional role for mammalian short interspersed elements, prototypical junk DNA.

Cox, G. S., D. W. Gutkin, M. J. Haas, and D. E. Cosgrove. 1998. Isolation of an Alu repetitive DNA binding protein and effect of CpG methylation on binding to its recognition sequence. Biochim Biophys Acta. 1396(1):67-87.

The structure, expression, and evolution of Alu repetitive DNA elements have been extensively studied, but the role of these sequences in the function of primate genomes has yet to be elucidated. The contribution of Alu repetitive sequences (ARS) to the structure, maintenance, or expression of the human genome is undoubtedly mediated by one or more DNA binding proteins. As part of a larger study in this laboratory to define the molecular mechanisms that result in de-repression of the glycoprotein hormone alpha-subunit (GPH alpha) gene in a variety of tumor cell types, it was found that the gene was hypermethylated in a variety of cell lines that produce alpha-subunit at high levels and significantly less methylated in cell lines where the gene is unexpressed or expressed at low levels. This is in sharp contrast to the majority of genes examined in this regard, which show an inverse correlation between methylation and expression. The analysis was extended to a group of clones isolated from a single cell line (HeLa) that were differentially methylated over the GPH alpha gene and exhibited a 400-fold range in its expression. These analyses demonstrated that methylation of a small number of CpG dinucleotides correlated with high level expression of the gene. Two of these sites are imbedded in oppositely oriented Alu repeats located in the 5'- flanking DNA and second intron. The upstream site was examined in some detail. DNase I footprint analysis demonstrated that the protein protects a region encompassing the sequence 5'-TTGAACCCGGGAG-3', and electrophoretic gel mobility shift analysis demonstrated specific binding of a protein to an oligonucleotide containing the DNase footprint sequence. Chromatography of nuclear extracts on Sephacryl S- 200, heparin--agarose, and oligonucleotide--Sepharose produced an apparently homogeneous preparation of the 50-53 kDa DNA-binding protein as judged by silver staining of sodium dodecylsulfate polyacrylamide gels. The affinity-purified material was enriched 15- to 18,000-fold over crude nuclear extracts. Binding of this protein to an oligonucleotide containing the DNase-protected sequence was severely inhibited when CpG dinucleotide in the Msp I recognition site was methylated on either the sense or antisense strands. Based on its properties, this protein has been termed MeSABp50 for methylation- sensitive Alu binding protein of 50 kDa.

Cronin, C. N., X. Zhang, D. A. Thompson, and W. S. McIntire. 1998. cDNA cloning of two splice variants of a human copper-containing monoamine oxidase pseudogene containing a dimeric Alu repeat sequence. Gene. 220(1-2):71-6.

Two alternatively spliced transcripts, psiHLAO1 and psiHLAO2, of a copper-containing monoamine oxidase pseudogene have been isolated from a human-liver cDNA library. The larger psiHLAO1 cDNA (2073bp) contains a 5'-flanking segment of 134bp, followed by an apparent open reading frame (ORF) of 1725bp. The deduced amino acid sequence of this ORF (574 residues) shares 81.0% similarity with the 763-residue monoamine oxidase from human placenta (HPAO) (the N-terminal 533 residues of psiHLAO1 share 86.7% similarity with HPAO). The psiHLAO1 ORF is interrupted by an in-frame stop codon corresponding to amino acid 225 and terminates within a type S(a) dimeric Alu repeat sequence. psiHLAO2 appears to be an alternatively spliced variant of psiHLAO1 that has 413 bases of psiHLAO1 excised according to the 'GT-AG' rule. The slightly longer 3' end of the psiHLAO2 transcript shows that the Alu repeat is followed by an 11-bp poly(A) tract that, in turn, is followed by an AT- rich (81%) sequence of 105bp. A reverse transcriptase-polymerase chain reaction (RT-PCR) protocol was used to confirm that both psiHLAO1 and psiHLAO2 are transcribed in human liver and placenta. A search of the expressed sequence tag (EST) database indicates that, like HPAO, psiHLAO derives also from the region 17q21 of the human genome.

Dhar, A., S. Gupta, and Y. D. Sharma. 1998. Alu elements in a Plasmodium vivax antigen gene. FEBS Lett. 423(2):193-7.

Plasmodium vivax is a very common human malaria parasite but it is poorly characterized at the molecular level. Here, we describe the isolation and characterization of an antigen coding gene of P. vivax which contains Alu elements. This gene, called Pv-Alu, is expressed during the erythrocytic phase of the parasite. The encoded 200 amino acid long polypeptide is highly hydrophobic, contains transmembrane domains, and is rich in leucine (19.4%), serine (15.9%), proline (15.4%) and phenylalanine (15.4%). The 5'-untranslated region and part of the 3'-end coding region of Pv-Alu show significant homology to different Alu families. The presence of Alu elements in the coding region of a parasite antigen gene is significant from a functional and evolutionary viewpoint.

Ferlini, A., N. Galie, L. Merlini, C. Sewry, A. Branzi, and F. Muntoni. 1998. A novel Alu-like element rearranged in the dystrophin gene causes a splicing mutation in a family with X-linked dilated cardiomyopathy. Am J Hum Genet. 63(2):436-46.

We have identified and characterized a genomic sequence with some features typical of Alu-like mobile elements rearranged into the dystrophin gene in a family affected by X-linked dilated cardiomyopathy. The Alu-like sequence rearrangement occurred 2.4 kb downstream from the 5' end of intron 11 of the dystrophin gene. This rearrangement activated one cryptic splice site in intron 11 and produced an alternative transcript containing the Alu-like sequence and part of the adjacent intron 11, spliced between exons 11 and 12. Translation of this alternative transcript is truncated because of the numerous stop codons present in every frame of the Alu-like sequence. Only the mutant mRNA was detected in the heart muscle, but in the skeletal muscle it coexisted with the normal one. This result is supported by the immunocytochemical findings, which failed to detect dystrophin in the patient's cardiac muscle but showed expression of a reduced level of protein in the skeletal muscle. Comparative analysis of the Alu-like sequence showed high homology with other repeated- element-containing regions and with several expressed sequence tags. We suggest that this Alu-like sequence could represent a novel class of repetitive elements, reiterated and clustered with some known mobile elements and capable of transposition. Our report underlines the complexity of the pathogenic mechanism leading to X-linked dilated cardiomyopathy but suggests that differences in tissue-specific expression of dystrophin mutations may be a common feature in this condition.

Goodier, J. L., and R. J. Maraia. 1998. Terminator-specific recycling of a B1-Alu transcription complex by RNA polymerase III is mediated by the RNA terminus-binding protein La. J Biol Chem. 273(40):26110-6.

Efficient synthesis of many small abundant RNAs is achieved by the proficient recycling of RNA polymerase (pol) III and stable transcription complexes. Cellular Alu and related retroposons represent unusual pol III genes that are normally repressed but are activated by viral infection and other conditions. The core sequences of these elements contain pol III promoters but must rely on fortuitous downstream oligo(dT) tracts for terminator function. We show that a B1- Alu gene differs markedly from a classical pol III gene (tRNAiMet) in terminator sequence requirements. B1-Alu genes that differ only in terminator sequence context direct differential RNA 3' end formation. These genes are assembled into stable transcription complexes but differ in their ability to be recycled in the presence of the La transcription termination factor. La binds to the nascent RNA 3' UUUOH end motif that is generated by transcriptional termination within the pol III termination signal, oligo(dT). We found that the recycling efficiency of the B1-Alu genes is correlated with the ability of La to access the 3' end of the nascent transcript and protect it from 3'-5' exonucleolytic processing. These results illuminate a relationship between RNA 3' end formation and transcription termination, and La- mediated reinitiation by pol III.

Greer, W. L., M. J. Dobson, P. E. Neumann, G. S. Girouard, S. M. Sparrow, and D. C. Riddell. 1998. FISH mapping and inter-Alu fingerprinting define the YAC contig map around the centromeric region of human chromosome 18. Genome. 41(3):468-70.

Previous reports concerning the location of D18S44 with respect to the centromere have been ambiguous. Also, it has not been possible, based on formerly reported markers, to show that contigs WC18.0 and WC18.1 overlap. However, the data presented here definitively show, using FISH technology, that D18S44 (located on WC18.0) maps to proximal 18q. Furthermore, inter-Alu fingerprinting shows a clear overlap between WC18.0 and WC18.1, thereby establishing a complete contig between D18S44 and markers from WC18.1.

Jabbari, K., and G. Bernardi. 1998. CpG doublets, CpG islands and Alu repeats in long human DNA sequences from different isochore families. Gene. 224(1-2):123-7.

A computer analysis of 946 human DNA sequences larger than 50kb and representing about 118Mb of DNA has led to the following observations. (i) Positive correlations hold between CpG levels and the GC levels of isochores and coding sequences, as expected from previous results. (ii) The correlation between CpG levels and the GC levels of pseudogenes is characterized by lower CpG values (at comparable GC levels) and by a lower slope compared with the correlation with coding sequences; this finding suggests that an extensive methylation followed by deamination has taken place on CpG doublets from inactive genes leading to a further CpG shortage. (iii) The frequency of CpG islands in long human sequences increases with increasing GC and almost parallels gene frequency. (iv) The frequency of Alu sequences also increases with increasing GC, but attains a maximum in H2 isochores, in agreement with previous experimental data. (v) The ratio 5mC/CpG (namely, the methylation level over available sites) decreases with increasing GC levels of isochores. This decrease is due only to a small extent to the increase of (unmethylated) CpG islands in GC-rich isochores, and takes place in spite of the increase of strongly methylated Alu sequences in GC-rich isochores; this stresses the much lower relative methylation (5mC/CpG) of single-copy sequences located in GC-rich isochores relative to those located in GC-poor isochores. (vi) CpG levels of Alus and CpG islands are positively correlated with the GC levels of the long sequences in which they are located. (vii) The CpG levels of both Alus and CpG islands increase with their GC levels.

Jeffs, A. R., S. M. Benjes, T. L. Smith, S. J. Sowerby, and C. M. Morris. 1998. The BCR gene recombines preferentially with Alu elements in complex BCR- ABL translocations of chronic myeloid leukaemia. Hum Mol Genet. 7(5):767-76.

Chronic myeloid leukaemia (CML) develops when two genes, BCR on chromosome 22 and ABL on chromosome 9, recombine to form a hybrid BCR- ABL gene with leukaemogenic properties. The mechanism which underlies this recombination is unknown, but additional chromosome sites may be involved to form complex BCR-ABL rearrangements. The majority of breakpoints in BCR occur within a 5 kb major breakpoint cluster region, M-Bcr. Here, we show that the 3' part of M-Bcr recombined within, or immediately adjacent to, Alu elements at the additional sites in all five complex BCR-ABL rearrangements that have been examined so far. This is a new finding which suggests that Alu sequences have an affinity for the BCR-ABL recombination process in complex rearrangements, and provides additional evidence for the association of these elements with somatic rearrangements which cause human leukaemia. We further show that sequence motifs similar to IgH switch pentamers and consensus binding sites of the lymphoid-associated Translin protein are present on one or more participating strands at 3'M-Bcr recombination sites. Motifs similar to Translin-binding sites were also identified within the Alu consensus. Expressed sequences mapped close to the breakpoint sites on other chromosomes in three of the five cases examined.

Levran, O., N. A. Doggett, and A. D. Auerbach. 1998. Identification of Alu-mediated deletions in the Fanconi anemia gene FAA. Hum Mutat. 12(3):145-52.

Fanconi anemia (FA) is an autosomal recessive syndrome associated with hypersensitivity to DNA cross-linking agents and predisposition to neoplasia. Eight complementation groups (A-H) have been described, but the only FA genes cloned so far are FAC and FAA. We have recently identified 40 different germline mutations, including microdeletions, microinsertions, and point mutations in genomic DNA from 97 FA patients from the International Fanconi Anemia Registry (IFAR) by single-strand conformational polymorphism (SSCP) analysis. Interestingly, only one mutant allele was identified in many of these patients. Haplotype analysis with intragenic polymorphisms, as well as cDNA analysis of some patients suggested the presence of large deletions that would not be detected by SSCP analysis. In this study, we report the occurrence of Alu-mediated genomic deletions in FAA. Two different deletions of 1.2 kb and 1.9 kb were found. Both deletions include exons 16 and 17 and remove a 156-bp segment from the transcript causing a shorter in- frame message. Sequence analysis revealed that introns 15 and 17 are rich in partial and complete Alu repeats. There are at least four head- to-tail arranged Alu elements in intron 17 and one in intron 15, all oriented in the 3'-->5' direction. Sequence analysis of the deletions showed that the 5' breakpoints occurred at different sites in the same Alu element in intron 15, while the 3' breakpoints were located in different Alu repeats in intron 17. Numerous Alu repeats are present in FAA, suggesting that Alu-mediated recombination might be an important mechanism for the generation of FAA mutations.

Novick, G. E., C. C. Novick, J. Yunis, E. Yunis, P. Antunez de Mayolo, W. D. Scheer, P. L. Deininger, M. Stoneking, D. S. York, M. A. Batzer, and R. J. Herrera. 1998. Polymorphic Alu insertions and the Asian origin of Native American populations. Hum Biol. 70(1):23-39.

A rapid PCR-based assay was used to study the distribution of 5 polymorphic Alu insertions in 895 unrelated individuals from 30 populations, 24 from North, Central, and South America. Although a significant level of interpopulation variability was detected, the variability was less than that observed in a worldwide population survey. This is consistent with the bottleneck effect and genetic drift forces that may have acted on the migrating founder groups. The results corroborate the Asian origin of native American populations but do not support the multiple-wave migration hypothesis supposedly responsible for the tri-partite Eskaleut, Nadene, and Amerind linguistic groups. Instead, these populations exhibit three major identifiable clusters reflecting geographic distribution. Close similarity between the Chinese and native Americans suggests recent gene flow from Asia.

Schmid, C. W. 1998. Does SINE evolution preclude Alu function? Nucleic Acids Res. 26(20):4541-50.

The evolution, mobility and deleterious genetic effects of human Alus are fairly well understood. The complexity of regulated transcriptional expression of Alus is becoming apparent and insight into the mechanism of retrotransposition is emerging. Unresolved questions concern why mobile, highly repetitive short interspersed elements (SINEs) have been tolerated throughout evolution and why and how families of such sequences are periodically replaced. Either certain SINEs are more successful genomic parasites or positive selection drives their relative success and genomic maintenance. A complete understanding of the evolutionary dynamics and significance of SINEs requires determining whether or not they have a function(s). Recent evidence suggests two possibilities, one concerning DNA and the other RNA. Dispersed Alus exhibit remarkable tissue-specific differences in the level of their 5-methylcytosine content. Differences in Alu methylation in the male and female germlines suggest that Alu DNA may be involved in either the unique chromatin organization of sperm or signaling events in the early embryo. Alu RNA is increased by cellular insults and stimulates protein synthesis by inhibiting PKR, the eIF2 kinase that is regulated by double-stranded RNA. PKR serves other roles potentially linking Alu RNA to a variety of vital cell functions. Since Alus have appeared only recently within the primate lineage, this proposal provokes the challenging question of how Alu RNA could have possibly assumed a significant role in cell physiology.

Slebos, R. J., M. A. Resnick, and J. A. Taylor. 1998. Inactivation of the p53 tumor suppressor gene via a novel Alu rearrangement. Cancer Res. 58(23):5333-6.

Inactivation of the p53 tumor suppressor gene is a common finding in human cancer. In most cases, inactivation is due to a point mutation in the gene, but rearrangement of the p53 gene is sometimes observed. We analyzed the inactivation of p53 in the human pancreas cancer cell line Hs766T, which harbors a structural alteration in the p53 gene. This inactivation was found to be the result of a complex deletion/insertion event involving at least two different Alu elements. The rearrangement eliminated exons 2-4 from the p53 gene, whereas a 175-bp Alu fragment was inserted between the breakpoints of the deletion. DNA sequence analysis of this Alu fragment revealed that it is identical to an Alu element in intron 1 of the p53 gene. This is the first report of p53 inactivation due to a rearrangement involving Alu elements. This type of inactivation may go unnoticed when only traditional methods to detect p53 alterations are used.

Strout, M. P., G. Marcucci, C. D. Bloomfield, and M. A. Caligiuri. 1998. The partial tandem duplication of ALL1 (MLL) is consistently generated by Alu-mediated homologous recombination in acute myeloid leukemia. Proc Natl Acad Sci U S A. 95(5):2390-5.

Chromosome abnormalities resulting in gene fusions are commonly associated with acute myeloid leukemia (AML), however, the molecular mechanism(s) responsible for these defects are not well understood. The partial tandem duplication of the ALL1 (MLL) gene is found in patients with AML and trisomy 11 as a sole cytogenetic abnormality and in 11% of patients with AML and normal cytogenetics. This defect results from the genomic fusion of ALL1 intron 6 or intron 8 to ALL1 intron 1. Here, we examined the DNA sequence at the genomic fusion in nine cases of AML with a tandem duplication of ALL1 spanning exons 2-6. Each breakpoint occurred within intron 6 of the ALL1 breakpoint cluster region and within a discrete 3.8-kb region near the 3' end of intron 1. In seven cases, a distinct point of fusion of intron 6 with intron 1 could not be identified. Instead, the sequence gradually diverged from an Alu element in intron 6 to an Alu element in intron 1 through a heteroduplex fusion. Thus, these rearrangements appear to be the result of a recombination event between homologous Alu sequences in introns 6 and 1. In two cases, the genomic junction was distinct and involved the fusion of a portion of an Alu element in intron 6 with non-Alu sequence in intron 1. These data support the hypothesis that a recombination event between homologous Alu sequences is responsible for the partial tandem duplication of ALL1 in the majority of AML cases with this genetic defect. Although Alu element-mediated homologous recombination events in germline cells are thought to be responsible for partial gene duplications or deletions in many inherited diseases, this appears to be the first demonstration identifying Alu element-mediated recombination as a consistent mechanism for gene rearrangement in somatic tissue.

Szmulewicz, M. N., G. E. Novick, and R. J. Herrera. 1998. Effects of Alu insertions on gene function. Electrophoresis. 19(8-9):1260-4.

Alu elements are a family of short interspersed repetitive elements (SINEs) found exclusively in primates. These elements are around 300 base pairs long, are found in excess of one million copies per diploid genome, and are dispersed throughout the human genome. Alu elements are scattered by a mechanism called "retrotransposition". Three independent steps are involved in retrotransposition: transcription of the Alu repetitive element, reverse transcription of the Alu RNA and integration of the Alu cDNA. The fact that Alu elements retrotranspose so readily suggests that they have a myriad of effects on the genome, mostly by inactivating genes or altering their function. These characteristics of Alu repetitive elements point to these repetitive DNA fragments as a major driving force for evolution. In addition, Alu elements are known to adopt diverse functions depending on the context of the surrounding genetic material into which they insert. In this article, we review some of the evidence that demonstrates the functional significance of Alu repeats.

Thomas, E., and R. J. Herrera. 1998. Multiplex polymerase chain reaction of Alu polymorphic insertions. Electrophoresis. 19(14):2373-9.

Alu sequences are present in humans in excess of 500,000 copies per haploid genome and represent the largest family of short interspersed repetitive elements (SINEs). These mobile genetic elements are ancestrally derived from the 7SL RNA gene and move throughout the genomes of primates by retroposition. Polymorphic Alu insertions have proven to be useful for population studies, paternity determinations and forensic applications. Additionally, a simple polymerase chain reaction (PCR)-based assay has been established to examine these polymorphisms. In the present study, we have applied the technique of multiplex polymerase chain reaction to the Alu polymorphic system. Duplex and triplex PCR reactions were performed for the analysis of five different Alu polymorphic loci in different combinations. This study represents a starting point for further experimentation to improve and eventually optimize Alu multiplex PCR.

Tsuchiya, T., Y. Saegusa, T. Taira, T. Mimori, S. M. Iguchi-Ariga, and H. Ariga. 1998. Ku antigen binds to Alu family DNA. J Biochem (Tokyo). 123(1):120-7.

The GC-rich segment containing GGAGGC (Alu core) is conserved within the RNA polymerase III (pol III) promoters of Alu family sequences. We have shown that the GGAGGC motif functions as a modulator of DNA replication as well as of transcription, and identified the proteins binding to the motif in human HeLa cells. In this study, the Alu core binding proteins were partially purified from human Raji cells by using an Alu core DNA affinity column. Both the proteins thus purified were implied to be subunits of Ku antigen based on the following criteria: The molecular weights of the proteins estimated on gel electrophoreses were 70 and 85 kDa, respectively, under denaturing conditions, while under non-denaturing conditions only one band was observed for the same sample at 150 kDa, probably representing hetero-dimer formed between the 70 and 85 kDa proteins. The sizes and the hetero-dimer formation are reminiscent of the 70 and 80 kDa subunits of Ku antigen (Ku-p70 and Ku-p80). Moreover, the purified proteins were immunoreactive with anti- Ku antibodies, and the specific DNA-protein complex on the Alu core element was cancelled by the anti-Ku antibodies. The nucleoprotein complex showed the same clipping patterns as those of the complex between the Alu core element and an authentically purified Ku antigen after proteolytic cleavage with trypsin and chymotrypsin.

Tvrdik, T., S. Marcus, S. M. Hou, S. Falt, P. Noori, N. Podlutskaja, F. Hanefeld, P. Stromme, and B. Lambert. 1998. Molecular characterization of two deletion events involving Alu- sequences, one novel base substitution and two tentative hotspot mutations in the hypoxanthine phosphoribosyltransferase (HPRT) gene in five patients with Lesch-Nyhan syndrome. Hum Genet. 103(3):311-8.

Mutations identified in the hypoxanthine phosphoribosyltransferase (HPRT) gene of patients with Lesch-Nyhan (LN) syndrome are dominated by simple base substitutions. Few hotspot positions have been identified, and only three large genomic rearrangements have been characterized at the molecular level. We have identified one novel mutation, two tentative hot spot mutations, and two deletions by direct sequencing of HPRT cDNA or genomic DNA from fibroblasts or T-lymphocytes from LN patients in five unrelated families. One is a missense mutation caused by a 610C-->T transition of the first base of HPRT exon 9. This mutation has not been described previously in an LN patient. A nonsense mutation caused by a 508C-->T transition at a CpG site in HPRT exon 7 in the second patient and his younger brother is the fifth mutation of this kind among LN patients. Another tentative hotspot mutation in the third patient, a frame shift caused by a G nucleotide insertion in a monotonous repeat of six Gs in HPRT exon 3, has been reported previously in three other LN patients. The fourth patient had a tandem deletion: a 57-bp deletion in an internally repeated Alu-sequence of intron 1 was separated by 14 bp from a 627-bp deletion that included HPRT exon 2 and was flanked by a 4-bp repeat. This complex mutation is probably caused by a combination of homologous recombination and replication slippage. Another large genomic deletion of 2969 bp in the fifth patient extended from one Alu-sequence in the promoter region to another Alu-sequence of intron 1, deleting the whole of HPRT exon 1. The breakpoints were located within two 39-bp homologous sequences, one of which overlapped with a well-conserved 26-bp Alu-core sequence previously suggested as promoting recombination. These results contribute to the establishment of a molecular spectrum of LN mutations, support previous data indicating possible mutational hotspots, and provide evidence for the involvement of Alu-mediated recombination in HPRT deletion mutagenesis.

Vervoort, R., R. Gitzelmann, W. Lissens, and I. Liebaers. 1998. A mutation (IVS8+0.6kbdelTC) creating a new donor splice site activates a cryptic exon in an Alu-element in intron 8 of the human beta- glucuronidase gene. Hum Genet. 103(6):686-93.

We have previously sequenced the complete coding region and the promoter region of the beta-glucuronidase gene of a patient with mild mucopolysaccharidosis type VII (MPS VII) and identified a nonsense mutation in the gene inherited from her mother. The mutation inherited from her father was not found. Here, we have extended the sequence analysis of the introns to cover all putative lariat branch points and putative intronic enhancers, although no nucleotide changes have been found in these regions. Careful analysis of mRNA structure by reverse transcription/polymerase chain reaction (RT-PCR) and direct sequencing has revealed the inclusion of a new exon derived from an antisense Alu- repeat in intron 8 and the skipping of exon 9 in a large proportion of the mRNA of our patient. A 2-bp deletion creating a strong 5'-splice site has subsequently been identified in the paternal gene of the patient (IVS8+0.6kbdelTC). With a sensitive RT-PCR assay, we demonstrate that both the inclusion of the Alu-cassette and the skipping of exon 9 are minor events in control samples and that mRNA with both alterations is only found in the IVS8+0.6kbdelTC carrier. The increased proportion of exon 9 skipping seems to be related to the premature termination of translation. This is the third report of a human disease mutation that creates a splice site and activates an antisense Alu-cassette; the question rises as to how these apparently strong cryptic exons are generally excluded from coding sequences.

Zietkiewicz, E., C. Richer, D. Sinnett, and D. Labuda. 1998. Monophyletic origin of Alu elements in primates. J Mol Evol. 47(2):172-82.

To get insight into the early evolution of the primate Alu elements, we characterized sequences of these repeats from the Malagasy prosimians, lemurs (Lemuridae) and sifakas (Indriidae), as well as from galagos (Lorisidae). These sequences were compared with the oldest Alu species known from the human genome: dimeric Alu J and S and free Alu monomers. Our analysis indicates that about 60 Myr ago, before the prosimian divergence, free left and right monomers formed an Alu heterodimer connected by a 19-nucleotide-long A-rich linker. The resulting elements successfully propagated in diverging primate lineages until about approximately 20 Myr ago, conserving similar sequence features and essentially the same Alu RNA secondary structure. We suggest that until that time the same "retropositional niche", molecular machinery making possible the proliferation by retroposition, constrained the evolution of Alu elements in extant primate species. These constraints became subsequently relaxed. In the Malagasy prosimians the dimeric Alu continued to amplify after acquiring a 34- to 36-nucleotide extension of their linker segment, whereas in the galago genome the "retropositional niche" was occupied by novel short elements.

Arcot, S. S., A. W. Adamson, G. W. Risch, J. LaFleur, M. B. Robichaux, J. E. Lamerdin, A. V. Carrano, and M. A. Batzer. 1998. High-resolution cartography of recently integrated human chromosome 19- specific Alu fossils. J Mol Biol. 281(5):843-56.

The recently inserted subfamilies of Alu retroposons (Ya5/8 and Yb8) are composed of approximately 2000 elements. We have screened a human chromosome 19-specific cosmid library for the presence of Ya5/8 and Yb8 Alu family members. This analysis resulted in the identification of 12 Ya5/8 Alu family members and 15 Yb8 Alu family members from human chromosome 19. The total number of Ya5/8 and Yb8 Alu family members located on human chromosome 19 does not differ from that expected based upon random integration of Alu repeats within the human genome. The distribution of both subfamilies of Alu elements along human chromosome 19 also appears to be random. DNA sequence analysis of the individual Alu elements revealed a low level of random mutations within both subfamilies of Alu elements consistent with their recent evolutionary origin. Oligonucleotide primers complementary to the flanking unique sequences adjacent to each Alu element were used in polymerase chain reaction assays to determine the phylogenetic distribution and human genomic variation associated with each Alu family member. All of the chromosome 19-specific Ya5/8 and Yb8 Alu family members were restricted to the human genome and absent from orthologous positions within the genomes of several non-human primates. Three of the Yb8 Alu family members were polymorphic for insertion presence/absence within the genomes of a diverse array of human populations. The polymorphic Alu elements will be useful tools for the study of human population genetics. Copyright 1998 Academic Press

Bai, M., N. Janicic, S. Trivedi, S. J. Quinn, D. E. Cole, E. M. Brown, and G. N. Hendy. 1997. Markedly reduced activity of mutant calcium-sensing receptor with an inserted Alu element from a kindred with familial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism. J Clin Invest. 99(8):1917-25.

Missense mutations have been identified in the coding region of the extracellular calcium-sensing receptor (CASR) gene and cause human autosomal dominant hypo- and hypercalcemic disorders. The functional effects of several of these mutations have been characterized in either Xenopus laevis oocytes or in human embryonic kidney (HEK293) cells. All of the mutations that have been examined to date, however, cause single putative amino acid substitutions. In this report, we studied a mutant CASR with an Alu-repetitive element inserted at codon 876, which was identified in affected members of families with the hypercalcemic disorders, familial hypocalciuric hypercalcemia (FHH) and neonatal severe hyperparathyroidism (NSHPT), to understand how this insertion affects CASR function. After cloning of the Alu-repetitive element into the wild-type CASR cDNA, we transiently expressed the mutant receptor in HEK293 cells. Expression of mutant and wild-type receptors was assessed by Western analysis, and the effects of the mutation on extracellular calcium (Ca2+(o)) and gadolinium (Gd3+(o)) elicited increases in the cytosolic calcium concentration (Ca2+(i)) were examined in fura-2-loaded cells using dual wavelength fluorimetry. The insertion resulted in truncated receptor species that had molecular masses some 30 kD less than that of the wild-type CASR and exhibited no Ca2+(i) responses to either Ca2+(o) or Gd3+(o). A similar result was observed with a mutated CASR truncated at residue 876. However, the Alu mutant receptor had no impact on the function of the coexpressed wild- type receptor. Interestingly, the Alu mutant receptor demonstrated decreased cell surface expression relative to the wild-type receptor, whereas the CASR (A877stop) mutant exhibited increased cell surface expression. Thus, like the missense mutations that have been characterized to date in families with FHH, the Alu insertion in this family is a loss-of-function mutation that produces hypercalcemia by reducing the number of normally functional CASRs on the surface of parathyroid and kidney cells. In vitro transcription of exon 7 of the CASR containing the Alu sequence yielded the full-length mutant product and an additional shorter product that was truncated due to stalling of the polymerase at the poly(T) tract. In vitro translation of the mutant transcript yielded three truncated protein products representing termination in all three reading frames at stop codons within the Alu insertion. Thus sequences within the Alu contribute to slippage or frameshift mutagenesis during transcription and/or translation.

Batzer, M. A., S. T. Sherry, P. L. Deininger, and M. Stoneking. 1997. Alu repeats and human evolution. Response. J Mol Evol. 45(1):7-8.

Berquin, I. M., M. Ahram, and B. F. Sloane. 1997. Exon 2 of human cathepsin B derives from an Alu element. FEBS Lett. 419(1):121-3.

Transcripts for the cysteine protease cathepsin B are alternatively spliced in the untranslated regions (UTRs). We show that a cathepsin B probe containing 5'-UTR sequences hybridized to an RNA of approximately 300 nt in addition to the typical 2.2 and 4.0 kbp mRNAs. Within this 5'- UTR, exon 2 was found to be homologous to Alu repetitive elements. Specifically, exon 2 was part of an Alu element interspersed with the cathepsin B gene. The approximately 300 nt band that hybridized to our cathepsin B probe likely corresponds to Alu transcripts, which are known to accumulate in human cells. Indeed, a similarly migrating band was detected with an authentic Alu probe. Thus, we suggest that primary transcripts for cathepsin B contain Alu sequences which are preserved as exon 2 in some fully spliced mRNAs.

Birse, D. E., U. Kapp, K. Strub, S. Cusack, and A. Aberg. 1997. The crystal structure of the signal recognition particle Alu RNA binding heterodimer, SRP9/14. Embo J. 16(13):3757-66.

The mammalian signal recognition particle (SRP) is an 11S cytoplasmic ribonucleoprotein that plays an essential role in protein sorting. SRP recognizes the signal sequence of the nascent polypeptide chain emerging from the ribosome, and targets the ribosome-nascent chain-SRP complex to the rough endoplasmic reticulum. The SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide RNA molecule. SRP9 and SRP14 proteins form a heterodimer that binds to the Alu domain of SRP RNA which is responsible for translation arrest. We report the first crystal structure of a mammalian SRP protein, that of the mouse SRP9/14 heterodimer, determined at 2.5 A resolution. SRP9 and SRP14 are found to be structurally homologous, containing the same alpha-beta-beta-beta-alpha fold. This we designate the Alu binding module (Alu bm), an additional member of the family of small alpha/beta RNA binding domains. The heterodimer has pseudo 2-fold symmetry and is saddle like, comprising a strongly curved six-stranded amphipathic beta-sheet with the four helices packed on the convex side and the exposed concave surface being lined with positively charged residues.

Bovia, F., N. Wolff, S. Ryser, and K. Strub. 1997. The SRP9/14 subunit of the human signal recognition particle binds to a variety of Alu-like RNAs and with higher affinity than its mouse homolog. Nucleic Acids Res. 25(2):318-26.

The heterodimeric subunit, SRP9/14, of the signal recognition particle (SRP) has previously been found to bind to scAlu and scB1 RNAs in vitro and to exist in large excess over SRP in anthropoid cells. Here we show that human and mouse SRP9/14 bind with high affinities to other Alu- like RNAs of different evolutionary ages including the neuron-specific BC200 RNA. The relative dissociation constants of the different RNA- protein complexes are inversely proportional to the evolutionary distance between the Alu RNA species and 7SL RNA. In addition, the human SRP9/14 binds with higher affinity than mouse SRP9/14 to all RNAs analyzed and this difference is not explained by the additional C- terminal domain present in the anthropoid SRP14. The conservation of high affinity interactions between SRP9/14 and Alu-like RNAs strongly indicates that these Alu-like RNPs exist in vivo and that they have cellular functions. The observation that human SRP9/14 binds better than its mouse counterpart to distantly related Alu RNAs, such as recently transposed elements, suggests that the anthropoid-specific excess of SRP9/14 may have a role in controlling Alu amplification rather than in compensating a defect in SRP assembly and functions.

Bui, N., N. Wolff, S. Cusack, and K. Strub. 1997. Mutational analysis of the protein subunits of the signal recognition particle Alu-domain. Rna. 3(7):748-63.

Two polypeptides of the murine signal recognition particle (SRP), SRP9 and SRP14, bind exclusively as a heterodimer to SRP RNA and their presence is required for elongation arrest activity of the particle. SRP9/14 also constitute a subunit of small cytoplasmic Alu RNPs. To identify RNA-binding determinants, we assayed the dimerization and RNA- binding capacities of altered proteins in vitro. Despite the structural homology of the two proteins, their requirements for dimerization differ substantially. In SRP9, an internal fragment of 43 amino acids is sufficient to allow dimer formation, whereas in SRP14 only few changes, such as removing an internal loop region, are tolerated without affecting its dimerization activity. The dimerization defect of the SRP14 proteins is most likely explained by a reduced stability or ability to fold of the proteins. Interestingly, SRP RNA can engage certain dimerization-defective SRP14 proteins into stable complexes, suggesting that low-affinity interactions between the RNA and SRP14 may help to overcome the folding defect or the reduced stability of the proteins. We identified two regions, one in each protein, that are essential for RNA-binding. In SRP9, acidic amino acid residues in the N- terminal alpha-helix and the adjacent loop and, in SRP14, a flexible internal loop region are critical for RNA-binding. In the heterodimer, the two regions are located in close proximity, consistent with the RNA- binding region being formed by both proteins.

Chae, J. J., Y. B. Park, S. H. Kim, S. S. Hong, G. J. Song, K. H. Han, Y. Namkoong, H. S. Kim, and C. C. Lee. 1997. Two partial deletion mutations involving the same Alu sequence within intron 8 of the LDL receptor gene in Korean patients with familial hypercholesterolemia. Hum Genet. 99(2):155-63.

Twenty-eight unrelated persons heterozygous for familial hypercholesterolemia (FH) were screened to assess the frequency and nature of major structural rearrangements at the low-density lipoprotein (LDL) receptor gene in Korean FH patients. Genomic DNA was analyzed by Southern blot hybridization with probes encompassing exons 1-18 of the LDL receptor gene. Two different deletion mutations (FH29 and FH110) were detected in three FH patients (10.7%). Each of the mutations was characterized by the use of exon-specific probes and detailed restriction mapping mediated by long-PCR (polymerase chain reaction). Mutation FH29 was a 3.83-kb deletion extending from intron 6 to intron 8 and FH110 was a 5.71-kb deletion extending from intron 8 to intron 12. In FH29, the translational reading frame was preserved and the deducible result was a cysteine-rich A and B repeat truncated protein that might be unable to bind LDL but would continue to bind beta-VLDL. FH110 is presumed to be a null allele, since the deletion shifts the reading frame and results in a truncated protein that terminates in exon 13. Sequence analysis revealed that both deletions have occurred between two Alu-repetitive sequences that are in the same orientation. This suggested that in these patients the deletions were caused by an unequal crossing over event following mispairing of two Alu sequences on different chromatids during meiosis. Moreover, in both deletions, the recombinations were related to an Alu sequence in intron 8 and the deletion breakpoints are found within a specific sequence, 27 bp in length. This supports the hypothesis that this region might have some intrinsic instability, and act as one of the important factors in large recombinational rearrangements.

Chang, D. Y., J. A. Newitt, K. Hsu, H. D. Bernstein, and R. J. Maraia. 1997. A highly conserved nucleotide in the Alu domain of SRP RNA mediates translation arrest through high affinity binding to SRP9/14. Nucleic Acids Res. 25(6):1117-22.

Binding of the signal recognition particle (SRP) to signal sequences during translation leads to an inhibition of polypeptide elongation known as translation arrest. The arrest activity is mediated by a discrete domain comprised of the Alu portion of SRP RNA and a 9 and 14 kDa polypeptide heterodimer (SRP9/14). Although very few nucleotides in SRP RNA are conserved throughout evolution, the remarkable conservation of G24, which resides in the region of SRP9/14 interaction, suggests that it is essential for translation arrest. To understand the functional significance of the G24 residue, we made single base substitutions in SRP RNA at this position and analyzed the ability of the mutants to bind SRP9/14 and to reconstitute functional SRPs. Mutation of G24 to C reduced binding to SRP9/14 by at least 50-fold, whereas mutation to A and U reduced binding approximately 2- and 5-fold respectively. The mutant RNAs could nevertheless assemble into SRPs at high subunit concentrations. SRPs reconstituted with mutant RNAs were not significantly defective in translation arrest assays, indicating that the conserved guanosine does not interact directly with the translational machinery. Taken together, these results demonstrate that G24 plays an important role in the translation arrest function of SRP by mediating high affinity binding of SRP9/14.

Chow, V. T., and H. H. Quek. 1997. Alpha coat protein COPA (HEP-COP): presence of an Alu repeat in cDNA and identity of the amino terminus to xenin. Ann Hum Genet. 61(Pt 4):369-73.

We previously sequenced the 4333-nucleotide cDNA of the COPA (HEP-COP) gene which encodes the human homologue of the alpha-subunit of the coatomer protein complex, involved in intracellular protein transport. Within the 3' untranslated region at nucleotides 4049-4333 was observed an Alu repeat containing conserved A and B block elements, and showing high homology to the human Alu-Sx subfamily consensus sequence. Upstream of the Alu repeat were noted a TATA box, a CAAT motif and two activating transcription factor (ATF)-like binding sites, which represent putative regulatory elements directing Alu transcription. In addition, the 25 and 35 N-terminal amino acid residues of COPA and its bovine homologue were identical to xenin-25 and proxenin, respectively. Xenin-25 is a gastrointestinal hormone that stimulates exocrine pancreatic secretion. This peptide is related to xenopsin, neurotensin and neuromedin N which are bioactive peptides derived from larger precursors via proteolytic cleavage by cathepsin E at processing sites determined by conserved C-terminal sequences, i.e. proline/valine-X-X- hydrophobic amino acid. Given the conformity of the C-terminal residues of xenin-25 (PWIL) and of its progenitor molecule, proxenin (VIQL), it is proposed that these peptides are generated by a similar mechanism of post-translational modification involving a parent precursor represented by the alpha-subunit of coatomer.

Cole, D. E., N. Janicic, S. R. Salisbury, and G. N. Hendy. 1997. Neonatal severe hyperparathyroidism, secondary hyperparathyroidism, and familial hypocalciuric hypercalcemia: multiple different phenotypes associated with an inactivating Alu insertion mutation of the calcium- sensing receptor gene [published erratum appears in Am J Med Genet 1997 Oct 17;72(2):251-2]. Am J Med Genet. 71(2):202-10.

Neonatal severe hyperparathyroidism (NSHPT) is considered an autosomal- recessive disorder, attributable in many cases to homozygous inactivating mutations of the Ca++-sensing receptor (CASR) gene at 3q13.3-21. Most heterozygotes are clinically asymptomatic but manifest as familial (benign) hypocalciuric hypercalcemia (FHH) with a laboratory profile that is variably and sometimes only marginally different from normal. In 5 NSHPT cases from 3 Nova Scotian families, we found homoallelic homozygosity for an insertion mutation in exon 7 of CASR that includes an Alu repeat element with an exceptionally long polyA tract. Four of the 5 NSHPT infants were treated by parathyroidectomy more than a decade ago and are well now. A fifth went undiagnosed until adulthood and has profound musculoskeletal and neurobehavioral deficits. Among 36 identified FHH heterozygotes are 3 individuals with an unexpected degree of hypercalcemia and elevated circulating parathyroid hormone levels consistent with secondary hyperparathyroidism. Two are obligately heterozygous offspring of NSHPT mothers with surgical hypoparathyroidism and variable compliance with vitamin D therapy. The other is an adult with coexistent celiac disease in whom hyperparathyroidism, probably secondary to vitamin D deficiency, led to surgery. In counseling affected families, the heterozygous state should not be considered entirely benign, since FHH heterozygotes, particularly infants, may be prone to secondary hyperparathyroidism and symptomatic hypercalcemia. In such families, molecular diagnosis will allow for unambiguous identification of at- risk individuals.

Cole, S. A., S. Birnbaum, and J. E. Hixson. 1997. Recent polymorphic insertion of an Alu repeat in the baboon lipoprotein lipase (LPL) gene. Gene. 193(2):197-201.

We have identified a polymorphic insertion in the lipoprotein lipase (LPL) gene in a captive baboon colony. Mapping and nucleotide (nt) sequence analysis of the polymorphism showed that it is due to the presence or absence of an Alu repetitive element in intron 7 of the baboon LPL gene. This polymorphic Alu repeat has not been reported in humans, and we did not detect the repeat in a survey of the LPL intron 7 gene region in other non-human primates. Comparison of nt at diagnostic positions in this Alu insertion with different Alu subfamily consensus sequences showed that it most closely resembles the young AluY subfamily. These data suggest that this polymorphic Alu repeat inserted independently in the baboon lineage.

Coullin, P., B. Andreo, J. P. Charlieu, J. J. Candelier, and F. Pellestor. 1997. Primed in situ (PRINS) labelling with Alu and satellite primers for rapid characterization of human chromosomes in hybrid cell lines. Chromosome Res. 5(5):307-12.

The primed in situ (PRINS) labelling method was developed as an alternative to classical cytogenetics and fluorescence in situ hybridization (FISH) for the characterization of interspecific somatic hybrids. Full karyotypes were performed by PRINS using Alu-specific primers to generate the painting of all human material associated with R-like banding. The representativity of individual human chromosomes was established using primers specific for discriminent alpha-satellite DNA sequences providing specific signals on the centromeres of the targeted chromosomes and corresponding spots in interphase nuclei. Using this methodology, a somatic hybrid clone was shown to be monochromosomal for the der(11) from a t(11;22) patient.

Englander, E. W., and B. H. Howard. 1997. Alu-mediated detection of DNA damage in the human genome. Mutat Res. 385(1):31-9.

A new approach to monitoring UV damage and repair in the human genome has been developed. The proposed approach is based on a combination of features unique to interspersed repetitive Alu elements, and the ability of certain DNA lesions to block Taq polymerase-mediated DNA synthesis: namely, the extraordinary abundance of Alu repeats throughout the human genome in conjunction with distinct sequence motifs comprising long runs of T residues which are likely targets for formation of UV lesions. Hence, Taq polymerase-mediated extension synthesis with Alu specific primers was employed to visualize formation of discrete predicted adducts within the element. Several variations of the Alu-primer driven amplification protocol were developed to monitor the following aspects of damage: (i) induction of UV-photoproducts at predicted sites within the Alu sequence, (ii) modification of extension synthesis profiles, (iii) UV dose dependent, quantitative inhibition of Alu-primer driven amplification. The assays reveal sites of predicted Taq polymerase blockage within the Alu sequence, a global decrease in the mean length of extension products, and a measurable reduction in the quantity of extension products that is inversely proportional to UV dose. Thus, the exceptional abundance of Alu repeats and their primary sequence features, in combination with the ability of UV lesions to block elongation by Taq polymerase, provide a novel and sensitive system for detecting UV damage in the human genome. The system detects UV damage at levels that are compatible with cellular DNA repair, and provides a unique amplification-based protocol for probing the overall integrity of human DNA.

Fuentes, J. J., C. Pucharcos, M. Pritchard, and X. Estivill. 1997. Alu-splice PCR: a simple method to isolate exon-containing fragments from cloned human genomic DNA. Hum Genet. 101(3):346-50.

We have developed a simple, straightforward procedure to isolate exons from cloned human genomic DNA. The method is PCR based and relies upon the conservation of splice-site sequences and the frequency of Alu repeat elements in the genome to capture coding sequences. We designed two different sets of primers: a primer from each end of the Alu element and primers with the 5' or 3' splice-site consensus sequences. Putative exons were amplified by PCR using YAC DNA as starting material. We applied Alu-splice PCR to two overlapping YACs, 72H9 and 860G11, from human chromosome 21. Sequence and northern analysis of 37 initial clones resulted in the identification of five novel exons.

Gaudieri, S., K. M. Giles, J. K. Kulski, and R. L. Dawkins. 1997. Duplication and polymorphism in the MHC: Alu generated diversity and polymorphism within the PERB11 gene family. Hereditas. 127(1-2):37-46.

The PERB11 gene family has at least five members within the telomeric region of the MHC. The PERB11.1 and PERB11.2 genes are approximately 40 kb and 160 kb centromeric of HLA-B, respectively. Using continuous genomic sequence encompassing PERB11.1 and PERB11.2, we have found a large (approximately 25 kb) segmental duplication extending beyond the genes themselves and other potential coding sequences. The major difference between the segments are large indels which are predominantly Alu sequences. The Alu sequences within the duplicated segments have created diversity via the internal and 3' poly A-rich region. A sequence comparison of an Alu sequence between two different human ancestral haplotypes shows a high level of polymorphism, particularly in the poly A-rich regions. This study characterises the Alu sequences within the peri-PERB11.1 and peri-PERB11.2 duplicated segments in relation to diversity and polymorphism and as evolutionary markers.

Gerber, A., M. A. O'Connell, and W. Keller. 1997. Two forms of human double-stranded RNA-specific editase 1 (hRED1) generated by the insertion of an Alu cassette. Rna. 3(5):453-63.

The double-stranded RNA-specific editase 1 (RED1/ADAR2) is implicated in the editing of precursor-mRNAs (pre-mRNA) encoding subunits of glutamate receptors (GluRs) in brain. Site-specific deamination of adenosine to inosine alters the codon at the Q/R site in GluR-B rendering the heteromeric receptor impermeable to Ca2+ ions. We cloned human RED1 (hRED1/hADAR2) cDNAs from a brain cDNA library. The human enzyme is 95% identical to the rat homologue. We characterized two alternatively spliced forms that differed by the presence of an Alu-J cassette in the deaminase domain. For the long form containing the Alu cassette, we isolated cDNA clones with an alternative C-terminus and 3'- UTR. An 8.8-kb transcript of hRED1 is most abundant in brain and heart, and lower levels are detected in other tissues. In vitro editing assays with purified recombinant hRED1 containing or lacking the Alu-J cassette revealed that both forms of the protein have the same substrate specificity, but differ in their catalytic activity.

Harteveld, K. L., M. Losekoot, R. Fodde, P. C. Giordano, and L. F. Bernini. 1997. The involvement of Alu repeats in recombination events at the alpha- globin gene cluster: characterization of two alphazero-thalassaemia deletion breakpoints. Hum Genet. 99(4):528-34.

Alu repetitive sequences are frequently involved in homologous and non- homologous recombination events in the alpha-cluster. Possible mechanisms involved in Alu-mediated recombination events are strand exchange, promoted by DNA pairing between highly homologous Alu repeats, and subsequent strand invasion. Alternatively, Alu sequences might play a more active role in recombinogenic processes in the alpha- cluster. We describe a novel 33-kb alphazero-thalassaemia deletion -- DUTCH encompassing the alpha- and zeta-globin genes and pseudogenes in a kindred of Dutch-Caucasian origin. This deletion appears similar, although not identical, to the previously described --MEDII deletion. Cloning and sequencing of both the --DUTCH and --MEDII deletion breakpoints clearly indicate that the mechanism leading to these alphazero-thalassaemia deletions involves misalignment between the highly homologous tandemly arranged Alu repeats at both parental sides, which are normally 33 kb apart. Comparison of breakpoint positions along the Alu consensus sequence indicate the involvement of a 26-bp core sequence in two out of five alphazero-thalassaemia deletions. This sequence has been identified by others as a possible hotspot of recombination. These findings favour the idea that Alu repeats stimulate recombination events not only by homologous pairing, but also by providing binding sites for recombinogenic proteins.

McKie, A. B., T. Iwamura, H. Y. Leung, M. A. Hollingsworth, and N. R. Lemoine. 1997. Alu-polymerase chain reaction genomic fingerprinting technique identifies multiple genetic loci associated with pancreatic tumourigenesis. Genes Chromosomes Cancer. 18(1):30-41.

DNA fingerprinting can be used to detect genetic rearrangements in cancer that may be associated with activation of oncogenes and inactivation of tumour suppressor genes. We have developed a fingerprinting strategy based on polymerase chain reaction (PCR) amplification of genomic DNA with primers specific for the Alu repeat sequences, which are highly abundant in the human genome. This has been applied to DNA from pancreatic cancer and paired normal samples to isolate and identify fragments of genomic DNA rearranged in the malignant cells. These fragments have been sequenced and used as probes to isolate hybridising clones from gridded bacteriophage P1, phage artificial chromosome, and cosmid libraries for fluorescent in situ hybridisation mapping and the identification of expressed sequences. Further characterisation has identified a putative novel gene (ART1) that is up-regulated specifically in pancreatic cancer as well as another sequence with similarity to genes involved in differentiation (POU domains). In conclusion, we suggest that Alu-PCR fingerprinting may be a useful technique for the identification of genes involved in tumourigenesis.

Mighell, A. J., A. F. Markham, and P. A. Robinson. 1997. Alu sequences. FEBS Lett. 417(1):1-5.

Alu sequences are frequently encountered during study of human genomic nucleic acid and form a major component of repetitive DNA. This review describes the origin of Alu sequences and their subsequent amplification and evolution into distinct subfamilies. In recent years a number of different functional roles for Alu sequences have been described. The multiple influences of Alu sequences on RNA polymerase II-mediated gene expression and the presence of Alu sequences in RNA polymerase III-generated transcripts are discussed.

Miniou, P., D. Bourc'his, D. Molina Gomes, M. Jeanpierre, and E. Viegas-Pequignot. 1997. Undermethylation of Alu sequences in ICF syndrome: molecular and in situ analysis. Cytogenet Cell Genet. 77(3-4):308-13.

The methylation status of young Alu sequences was investigated in four ICF patients. In fibroblast and leukocyte DNAs, Alu repeats were either undermethylated (HhaI and HpaII digestion) or demethylated (BstUI digestion), in contrast with the methylated status of Alus in control subjects. The methylation profile exhibited in ICF patients reproduces the normal profile of placental or sperm DNA. High-sensitivity immunocytochemical detection of HhaI and HpaII restriction sites on metaphase chromosomes provided further evidence of this undermethylation. The DNA methylation defect in ICF patients, first detected in satellite DNAs (constitutive heterochromatin) and CpG islands of genes on the inactive X chromosome (facultative heterochromatin), thus includes Alu sequences that are widely distributed throughout the human genome.

Nobukuni, T., M. Kobayashi, A. Omori, S. Ichinose, T. Iwanaga, I. Takahashi, K. Hashimoto, S. Hattori, K. Kaibuchi, Y. Miyata, T. Masui, and S. Iwashita. 1997. An Alu-linked repetitive sequence corresponding to 280 amino acids is expressed in a novel bovine protein, but not in its human homologue. J Biol Chem. 272(5):2801-7.

A novel protein harboring a 280-amino acid region from an Alu-linked repetitive sequence (bovine Alu-like dimer-driven family) was isolated from a bovine brain S-100 fraction using monoclonal antibodies against a rat GTPase-activating protein that shares the same epitope. The protein has an apparent molecular mass of 97 kDa (p97). Western blot analysis using extracts prepared from various tissues showed p97 to be predominantly detected in brain and moderately in liver and lung. From sequence analysis of the cDNA encoding p97, it was found that the 840- base pair sequence homologous to a part of the bovine Alu-like dimer- driven family, which has never been shown to be expressed, occurs in the middle of the protein coding region. The protein also contains a pair of intramolecular repeats composed of 40 highly hydrophilic amino acids at the C terminus. Human cDNA homologous to p97 was cloned, and its nucleotide sequence demonstrates that the 840-base pair repetitive sequence and one of the intramolecular repeats are missing. We named p97 bovine BCNT after Bucentaur. These results show that bovine BCNT is a unique molecule and suggest that an analysis of the relationship between bovine bcnt and its human homologue may help further the understanding of gene organization and evolution.

Puget, N., D. Torchard, O. M. Serova-Sinilnikova, H. T. Lynch, J. Feunteun, G. M. Lenoir, and S. Mazoyer. 1997. A 1-kb Alu-mediated germ-line deletion removing BRCA1 exon 17. Cancer Res. 57(5):828-31.

Although more than 100 different BRCA1 germ-line mutations have already been identified in breast and/or ovarian cancer families, we report for the first time a deleterious genomic rearrangement in BRCA1. A 1-kb deletion comprising exon 17 was found in a large breast and ovarian cancer family, leading to a frameshift in the mutant mRNA due to the absence of exon 17. This deletion is probably the result of a recombination between two closely related Alu sequences. It was not detected by conventional PCR-based methods involving the genomic screening of the 22 coding exons or reverse transcription-PCR because the transcript without exon 17 is unstable in lymphoblastoid cell lines. Therefore, rearrangements in the BRCA1 gene should be sought in breast/ovarian cancer families in which no mutations have been found by PCR-based methods in the coding region or in the splice sites.

Renwick, P. J., A. J. Birley, and M. A. Hulten. 1997. Study of Alu sequences at the hypoxanthine phosphoribosyltransferase (hprt) encoding region of man. Gene. 184(2):155-62.

The hypoxanthine phosphoribosyltransferase (hprt) encoding region of man is considered rich in Alu sequences: with 49 sequences present within 57 kilobases. Subfamily classification of the Alu sequences and identification of flanking direct repeats has been carried out to detect past rearrangements associated with their insertion into the region. Members of the Alu-J and three Alu-S subfamilies are present, along with the existence of free left arm sequences. Using available data, a comparison is made of the Alu subfamilies present at different gene regions. The heterogeneity in the number of each subfamily present at different genes shows that no one particular subfamily attained saturation in the genome. Several adjacent insertions of Alu sequences are seen at the hprt region. Furthermore two novel sequences are described, there is an incident where one Alu sequence has inserted into the middle poly(A) tract of an existing sequence at the hprt region; while another result from an Alu/Alu cross-over event elsewhere in the genome, before insertion into the hprt region. Once inserted, the Alu sequences are rarely subject to loss or rearrangement.

Ridker, P. M., M. T. Baker, C. H. Hennekens, M. J. Stampfer, and D. E. Vaughan. 1997. Alu-repeat polymorphism in the gene coding for tissue-type plasminogen activator (t-PA) and risks of myocardial infarction among middle-aged men. Arterioscler Thromb Vasc Biol. 17(9):1687-90.

An Alu-repeat polymorphism in the gene coding for tissue-type plasminogen activator has been described recently, and it has been hypothesized that this polymorphism may predict risk of coronary thrombosis. In a prospective cohort of nearly 15,000 apparently healthy men, presence of an Alu-repeat insertion/deletion (I/D) polymorphism in the gene coding for tissue-type plasminogen activator was determined among 369 study participants who subsequently suffered a first myocardial infarction (cases) and among a group of 369 age- and smoking- matched study participants who remained free of reported cardiovascular disease during follow-up (controls). The distributions of the II, DI, and DD genotypes of the tissue-type plasminogen activator polymorphism among men who subsequently suffered myocardial infarction (0.30, 0.50, 0.21) were virtually identical to those who remained free of disease (0.29, 0.50, 0.21; P = .9). There was no evidence of association between the Alu insertion polymorphism and risks of future myocardial infarction in models assuming either allelic recessive (relative risk, 1.05; 95% confidence interval, 0.8 to 1.4, P = .8) or allelic dominant (relative risk, 1.04; 95% confidence interval, 0.7 to 1.5, P = .8) modes of inheritance, nor were associations found in analyses stratified by age, family history, hypercholesterolemia, or the presence of other risk factors for premature coronary disease. Multivariate analysis had no important effects on these relationships. In this cohort of middle-aged US men, the presence of the insertion allele of the Alu-repeat polymorphism of the tissue-type plasminogen activator gene is not associated with future risks of myocardial infarction.

Rothberg, P. G., S. Ponnuru, D. Baker, J. F. Bradley, A. I. Freeman, G. W. Cibis, D. J. Harris, and D. P. Heruth. 1997. A deletion polymorphism due to Alu-Alu recombination in intron 2 of the retinoblastoma gene: association with human gliomas. Mol Carcinog. 19(2):69-73.

The retinoblastoma gene (RB) encodes a tumor suppressor that is inactivated in a number of different types of cancer. We searched for gross alterations of this gene in tumors of the central nervous system by using Southern blot hybridization. A common alteration was found in several tumors and was mapped to the region around exon 2. Nucleotide sequencing showed that the alteration was caused by a 799-bp deletion in intron 2 of the RB gene and was probably due to homologous recombination between two Alu repeats. Deletions of this type have not been found previously in the RB gene. The deletion turned out to be a polymorphism with an allele frequency estimated at 2.2% in 185 patients without cancer. The deletion was found in five of 48 patients with brain tumors (allele frequency of 5.2%). This difference is not statistically significant (P = 0.149, Fisher's exact test). Confining the analysis only to glioma brain tumors revealed a statistically significant difference compared with the cancer-free patient controls (P = 0.027, Fisher's exact test). Further study is needed to determine if the deletion is a weak brain cancer-predisposing mutation or a harmless polymorphism. Finding this mutation in a tumor and the germline DNA of a retinoblastoma patient could lead to incorrect estimation of the heritability of a tumor.

Sarrowa, J., D. Y. Chang, and R. J. Maraia. 1997. The decline in human Alu retroposition was accompanied by an asymmetric decrease in SRP9/14 binding to dimeric Alu RNA and increased expression of small cytoplasmic Alu RNA. Mol Cell Biol. 17(3):1144-51.

Alu interspersed elements are inserted into the genome by a retroposition process that occurs via dimeric Alu RNA and causes genetic disorders in humans. Alu RNA is labile and can be diverted to a stable left monomer transcript known as small cytoplasmic Alu (scAlu) RNA by RNA 3' processing, although the relationship between Alu RNA stability, scAlu RNA production, and retroposition has been unknown. In vivo, Alu and scAlu transcripts interact with the Alu RNA-binding subunit of signal recognition particle (SRP) known as SRP9/14. We examined RNAs corresponding to Alu sequences that were differentially active during primate evolution, as well as an Alu RNA sequence that is currently active in humans. Mutations that accompanied Alu RNA evolution led to changes in a conserved structural motif also found in SRP RNAs that are associated with thermodynamic destabilization and decreased affinity of the Alu right monomer for SRP9/14. In contrast to the right monomer, the Alu left monomer maintained structural integrity and high affinity for SRP9/14, indicating that scAlu RNA has been under selection during human evolution. Loss of Alu right monomer affinity for SRP9/14 is associated with scAlu RNA production from Alu elements in vivo. Moreover, the loss in affinity coincided with decreased rates of Alu amplification during primate evolution. This indicates that stability of the Alu right monomer is a critical determinant of Alu retroposition. These results provide insight into Alu mobility and evolution and into how retroposons may interact with host proteins during genome evolution.

Shaikh, T. H., A. M. Roy, J. Kim, M. A. Batzer, and P. L. Deininger. 1997. cDNAs derived from primary and small cytoplasmic Alu (scAlu) transcripts. J Mol Biol. 271(2):222-34.

We have isolated and sequenced twenty-six cDNAs derived from primary Alu transcripts. Most cDNAs (22/26) sequenced end in multiple T residues, known to be at the termination for RNA polymerase III- directed transcripts. We conclude that these cDNAs were derived from authentic, RNA polymerase III-directed primary Alu transcripts. Sequence alignment of the cDNAs with Alu consensus sequences show that the cDNAs belong to different, previously described Alu subfamilies. The sequence variation observed in the 3' non-Alu regions of each of the cDNAs led us to conclude that they were derived from different genomic loci, thus demonstrating that multiple Alu loci are transcriptionally active. The subfamily distribution of the cDNAs suggests that transcriptional activity is biased towards evolutionarily younger Alu subfamilies, with a strong selection for the consensus sequence in the first 42 bases and the promoter B box. Sequence data from seven cDNAs derived from small cytoplasmic Alu (scAlu) transcripts, a processed form of Alu transcripts, also have a similar bias towards younger Alu subfamilies. About half of these cDNAs are due to processing or degradation, but the other half appear to be due to the formation of a cryptic RNA polymerase III termination signal in multiple loci. Using our sequence data, we have isolated a transcriptionally active genomic Alu element belonging to the Ya5 subfamily. In vitro transcription studies of this element suggest that its flanking sequences contribute to its transcriptional activity. The role of flanking sequences and other factors involved in transcriptional activity of Alu elements are discussed.

Sherry, S. T., H. C. Harpending, M. A. Batzer, and M. Stoneking. 1997. Alu evolution in human populations: using the coalescent to estimate effective population size. Genetics. 147(4):1977-82.

There are estimated to be approximately 1000 members of the Ya5 Alu subfamily of retroposons in humans. This subfamily has a distribution restricted to humans, with a few copies in gorillas and chimpanzees. Fifty-seven Ya5 elements were previously cloned from a HeLa-derived randomly sheared total genomic library, sequenced, and screened for polymorphism in a panel of 120 unrelated humans. Forty-four of the 57 cloned Alu repeats were monomorphic in the sample and 13 Alu repeats were dimorphic for insertion presence/absence. The observed distribution of sample frequencies of the 13 dimorphic elements is consistent with the theoretical expectation for elements ascertained in a single diploid cell line. Coalescence theory is used to compute expected total pedigree branch lengths for monomorphic and dimorphic elements, leading to an estimate of human effective population size of approximately 18,000 during the last one to two million years.

So, C. W., Z. G. Ma, C. M. Price, S. Dong, S. J. Chen, L. J. Gu, C. K. So, L. M. Wiedemann, and L. C. Chan. 1997. MLL self fusion mediated by Alu repeat homologous recombination and prognosis of AML-M4/M5 subtypes. Cancer Res. 57(1):117-22.

Fifty-six patients with de novo acute myeloid leukemia M4/M5 subtypes were studied for rearrangements of the mixed lineage leukemia gene, MLL (also called HRX, Htrx-1, or ALL-1). Ten patients (18%) showed rearrangements of the MLL gene, 9 in a major breakpoint cluster region within a centromeric 8.3-kb BamHI fragment, whereas rearrangement in one patient was the result of a direct tandem duplication of exons 2-6 of MLL. Analysis of sequences at the duplication junction revealed that the points of MLL fusion within introns 6 and 1 both lie within Alu elements. This suggests the involvement of Alu repeat mediated homologous recombination in MLL self fusion. For the 10 rearranged samples, cytogenetics analysis revealed a normal karyotype in 3, and 3 had abnormalities other than 11q23. Survival analysis of patients revealed no difference between those with rearrangement of MLL and those showing the germ-line configuration.

Stanley, S. E. 1997. Alu repeats and human evolution. J Mol Evol. 45(1):6-7.

Stefanescu, G., M. Caraghin, N. Azoitei, and A. Azoitei. 1997. Preliminary estimation of the Y Alu polymorphic (YAP) element in the Romanian population. Gene Geogr. 11(1):47-50.

We analyzed the polymorphism for the presence/absence of the YAP element in two male Romanian samples. Frequencies of 3.7% and 10.5% were found for the presence of the element in Maramures (North Romania) and Vrancea (East Romania).

Stoneking, M., J. J. Fontius, S. L. Clifford, H. Soodyall, S. S. Arcot, N. Saha, T. Jenkins, M. A. Tahir, P. L. Deininger, and M. A. Batzer. 1997. Alu insertion polymorphisms and human evolution: evidence for a larger population size in Africa. Genome Res. 7(11):1061-71.

Alu insertion polymorphisms (polymorphisms consisting of the presence/absence of an Alu element at a particular chromosomal location) offer several advantages over other nuclear DNA polymorphisms for human evolution studies. First, they are typed by rapid, simple, PCR-based assays; second, they are stable polymorphisms-newly inserted Alu elements rarely undergo deletion; third, the presence of an Alu element represents identity by descent-the probability that different Alu elements would independently insert into the exact same chromosomal location is negligible; and fourth, the ancestral state is known with certainty to be the absence of an Alu element. We report here a study of 8 loci in 1500 individuals from 34 worldwide populations. African populations exhibit the most between-population differentiation, and the population tree is rooted in Africa; moreover, the estimated effective time of separation of African versus non-African populations is 137,000 +/- 15,000 years ago, in accordance with other genetic data. However, a principal coordinates analysis indicates that populations from Sahul (Australia and New Guinea) are nearly as close to the hypothetical ancestor as are African populations, suggesting that there was an early expansion of tropical populations of our species. An analysis of heterozygosity versus genetic distance suggests that African populations have had a larger effective population size than non-African populations. Overall, these results support the African origin of modern humans in that an earlier expansion of the ancestors of African populations is indicated.

Toda, Y., and M. Tomita. 1997. Alu elements as an aid in deciphering genome rearrangements. Gene. 205(1-2):173-6.

Genomic rearrangements result in genomic duplications that lead to the generation of more complex genomes. Some attempts have been made to trace duplication histories of different loci using Alu elements because of their large population in primate genomes (Chen et al., 1989; Mnukova-Fajdelova et al., 1994). In this short report, using the human growth hormone locus as an example, we demonstrate the usefulness of Alu repetitive elements in computer sequence analyses when tracing duplication histories. Information on subfamily classification, direction, arrangements, Poly(A) tails and direct repeats can aid our understanding of genome rearrangements.

Weichenrieder, O., U. Kapp, S. Cusack, and K. Strub. 1997. Identification of a minimal Alu RNA folding domain that specifically binds SRP9/14. Rna. 3(11):1262-74.

We have identified functionally and analyzed a minimal Alu RNA folding domain that is recognized by SRPphi14-9. Recombinant SRPphi14-9 is a fusion protein containing on a single polypeptide chain the sequences of both the SRP14 and SRP9 proteins that are part of the Alu domain of the signal recognition particle (SRP). SRPphi14-9 has been shown to bind to the 7SL RNA of SRP and it confers elongation arrest activity to reconstituted SRP in vitro. Alu RNA variants with homogeneous 3' ends were produced in vitro using ribozyme technology and tested for specific SRPphi14-9 binding in a quantitative equilibrium competition assay. This enabled identification of an Alu RNA of 86 nt (SA86) that competes efficiently with 7SL RNA for SRPphi14-9 binding, whereas smaller RNAs did not. The secondary structure of SA86 includes two stem- loops that are connected by a highly conserved bulge and, in addition, a part of the central adaptor stem that contains the sequence at the very 3' end of 7SL RNA. Circularly permuted variants of SA86 competed only if the 5' and 3' ends were joined with an extended linker of four nucleotides. SA86 can thus be defined as an autonomous RNA folding unit that does not require its 5' and 3' ends for folding or for specific recognition by SRPphi14-9. These results suggest that Alu RNA identity is determined by a characteristic tertiary structure, which might consist of two flexibly linked domains.

Yandava, C. N., J. M. Gastier, J. C. Pulido, T. Brody, V. Sheffield, J. Murray, K. Buetow, and G. M. Duyk. 1997. Characterization of Alu repeats that are associated with trinucleotide and tetranucleotide repeat microsatellites. Genome Res. 7(7):716-24.

The association of subclasses of Alu repetitive elements with various classes of trinucleotide and tetranucleotide microsatellites was characterized as a first step toward advancing our understanding of the evolution of microsatellite repeats. In addition, information regarding the association of specific classes of microsatellites with families of Alu elements was used to facilitate the development of genetic markers. Sequences containing Alu repeats were eliminated because unique primers could not be designed. Various classes of microsatellites are associated with different classes of Alu repeats. Very abundant and poly(A)-rich microsatellite classes (ATA, AATA) are frequently associated with an evolutionarily older subclass of Alu repeats, AluSx, whereas most of GATA and CA microsatellites are associated with a recent Alu subfamily, AluY. Our observations support all three possible mechanisms for the association of Alu repeats to microsatellites. Primers designed using a set of sequences from a particular microsatellite class showed higher homology with more sequences of that class than probes designed for other classes. We developed an efficient method of prescreening GGAA and ATA microsatellite clones for Alu repeats with probes designed in this study. We also showed that Alu probes labeled in a single reaction (multiplex labeling) could be used efficiently for prescreening of GGAA clones. Sequencing of these prescreened GGAA microsatellites revealed only 5% Alu repeats. Prescreening with primers designed for ATA microsatellite class resulted in the reduction of the loss of markers from approximately 50% to 10%. The new Alu probes that were designed have also proved to be useful in Alu-Alu fingerprinting.

Zucman-Rossi, J., M. A. Batzer, M. Stoneking, O. Delattre, and G. Thomas. 1997. Interethnic polymorphism of EWS intron 6: genome plasticity mediated by Alu retroposition and recombination. Hum Genet. 99(3):357-63.

The EWS gene has been identified as being systematically translocated in Ewing's sarcoma. In order to ascertain the basis of a marked interethnic difference in the incidence of Ewing's sarcoma, intron 6 of EWS, which is located near the translocation breakpoint region (EWSR1), was characterized. Sequence analysis of the entire intron 6 region revealed a very high density of Alu elements. Most of these Alu sequences could be classified in previously described subfamilies, facilitating delineation of an evolutionary model that involves successive retroposition events. According to this model, the EWS intron 6 region progressively expanded until about 5 million years ago. More recently (10(5) years ago), in part of the human population, the size of this region decreased by over 50% as the result of a homeologous recombination between two Alu sequences, which removed 2480 bp. This rare allele has only been observed in individuals of African origin, a population that is characterized by the lowest incidence of Ewing's sarcoma.

Arcot, S. S., M. M. DeAngelis, S. T. Sherry, A. W. Adamson, J. E. Lamerdin, P. L. Deininger, A. V. Carrano, and M. A. Batzer. 1997. Identification and characterization of two polymorphic Ya5 Alu repeats. Mutat Res. 382(1-2):5-11.

Two new polymorphic Alu elements (HS2.25 and HS4.14) belonging to the young (Ya5/8) subfamily of human-specific Alu repeats have been identified. DNA sequence analysis of both Alu repeats revealed that each Alu repeat had a long 3'-oligo-dA-rich tail (41 and 52 nucleotides in length) and a low level of random mutations. HS2.25 and HS4.14 were flanked by short precise direct repeats of 8 and 14 nucleotides in length, respectively. HS2.25 was located on human chromosome 13, and HS4.14 on chromosome 1. Both Alu elements were absent from the orthologous positions within the genomes of non-human primates, and were highly polymorphic in a survey of twelve geographically diverse human groups.

Baban, S., J. D. Freeman, and D. L. Mager. 1996. Transcripts from a novel human KRAB zinc finger gene contain spliced Alu and endogenous retroviral segments. Genomics. 33(3):463-72.

During the course of an investigation into the potential effects of endogenous retroviruses on adjacent gene expression, we isolated two cDNA clones containing a small sequence segment belonging to the human endogenous retrovirus family, HERV-H. Characterization of the clones revealed that they represent transcripts from a novel KRAB zinc finger gene termed ZNF177. The two cDNA clones differ at their 5' termini and in the presence of a 559-bp internal exon. The clone containing this internal exon has six imperfect zinc finger motifs followed by seven perfect copies of the C2H2 type but has a frame shift between the KRAB domain and the downstream zinc finger region. The smaller clone lacks the six imperfect motifs and has an intact ORF. The 5' putative untranslated regions of both cDNAs contain an 86-bp HERV-H env segment and a segment of an Alu repeat, both in the antisense orientation, that have been incorporated by splicing. RT-PCR experiments show evidence of alternative splicing but the majority of transcripts appear to contain the Alu and env segments. Genomic PCR and hybridization experiments suggest that a partial HERV-H element is integrated within the ZNF177 locus, which Southern analysis has shown to be a single-copy gene. Northern and RT-PCR analyses suggest that ZNF177 is transcribed at a low level in a variety of cell types.

Batzer, M. A., S. S. Arcot, J. W. Phinney, M. Alegria-Hartman, D. H. Kass, S. M. Milligan, C. Kimpton, P. Gill, M. Hochmeister, P. A. Ioannou, R. J. Herrera, D. A. Boudreau, W. D. Scheer, B. J. Keats, P. L. Deininger, and M. Stoneking. 1996. Genetic variation of recent Alu insertions in human populations. J Mol Evol. 42(1):22-9.

The Alu family of interspersed repeats is comprised of over 500,000 members which may be divided into discrete subfamilies based upon mutations held in common between members. Distinct subfamilies of Alu sequences have amplified within the human genome in recent evolutionary history. Several individual Alu family members have amplified so recently in human evolution that they are variable as to presence and absence at specific loci within different human populations. Here, we report on the distribution of six polymorphic Alu insertions in a survey of 563 individuals from 14 human population groups across several continents. Our results indicate that these polymorphic Alu insertions probably have an African origin and that there is a much smaller amount of genetic variation between European populations than that found between other population groups.

Batzer, M. A., P. L. Deininger, U. Hellmann-Blumberg, J. Jurka, D. Labuda, C. M. Rubin, C. W. Schmid, E. Zietkiewicz, and E. Zuckerkandl. 1996. Standardized nomenclature for Alu repeats. J Mol Evol. 42(1):3-6.

Chang, D. Y., K. Hsu, and R. J. Maraia. 1996. Monomeric scAlu and nascent dimeric Alu RNAs induced by adenovirus are assembled into SRP9/14-containing RNPs in HeLa cells. Nucleic Acids Res. 24(21):4165-70.

Nearly 1 000 000 copies of Alu interspersed elements comprise approximately 5% of human DNA. Alu elements cause gene disruptions by a process known as retrotransposition, in which dimeric Alu RNA is a presumed intermediate. Dimeric Alu transcripts are labile, giving rise to stable left monomeric scAlu RNAs whose levels are tightly regulated. Induction of Alu RNA by viral infection or cell stress leads to a dramatic increase in dimeric Alu transcripts, while scAlu RNA increases modestly. Each monomer of the dimeric Alu element shares sequence homology with the 7SL RNA component of the signal recognition particle (SRP). The SRP protein known as SRP9/14 is also found in a discrete complex with scAlu RNA, although whether dimeric Alu RNA is associated with SRP9/14 had been unknown. Here we show that antiserum to human SRP9 immunoprecipitates both scAlu RNA and dimeric Alu RNAs and that these RNPs accumulate after adenovirus infection, while levels of SRP9, SRP14, SRP54 and 7SL SRP RNA are unaffected. Dimeric Alu RNAs are also associated with the La protein, indicating that these are indeed nascent RNA polymerase III transcripts. This report documents that induced Alu transcripts are assembled into SRP9/14-containing RNPs in vivo while SRP levels are unchanged. Implications for Alu RNA metabolism and evolution are discussed.

Chesnokov, I., and C. W. Schmid. 1996. Flanking sequences of an Alu source stimulate transcription in vitro by interacting with sequence-specific transcription factors. J Mol Evol. 42(1):30-6.

An Alu source gene, called the EPL Alu, was previously isolated by a phylogenetic strategy. Sequences flanking the EPL Alu family member stimulate its RNA polymerase III (Pol III) template activity in vitro. One cis-acting element maps within a 40-nucleotide region immediately upstream to the EPL Alu. This same region contains an Ap1 site which, when mutated, abolishes the transcriptional stimulation provided by this region. The flanking sequence, as assayed by gel mobility shift, forms sequence-specific complexes with several nuclear factors including Ap1. These results demonstrate that an an ancestral Alu source sequence fortuitously acquired positive transcriptional control elements by insertion into the EPL locus, thereby providing biochemical evidence for a model which explains the selective amplification of Alu subfamilies.

Chiang, Y., and J. K. Vishwanatha. 1996. Characterization of the HeLa cell 35 kDa Alu-element binding protein. Mol Cell Biochem. 155(2):131-8.

Human Alu-elements are short interspersed DNA sequences that comprise approximately 5% of the human genome. The physiological role of Alu- elements are unknown, although they are proposed to be involved in DNA replication, transcriptional regulation and nuclear transport of signal recognition particle RNA. Proteins that bind to Alu-element and Alu RNA have been identified in human cells. In HeLa cells, two proteins of 120 kDa and 35 kDa specifically bind to Alu-elements. We find that the 35 kDa protein is localized exclusively to the nucleus, while the 120 kDa protein is distributed between nucleus and cytoplasm. The 35 kDa protein is regulated by phosphorylation. Upon dephosphorylation, its DNA binding activity is significantly enhanced. Contrary to the recent identification of the smaller Alu-element binding protein as annexin II, we find that annexin II is not an Alu-element binding protein. Using a variety of techniques, we demonstrate that the 35 kDa Alu- element binding protein is distinct from annexin II.

Clawson, G. A., S. L. Schalles, G. Wolz, J. Weisz, T. M. Crone, and G. Q. Miranda. 1996. Focal altered compartmentation of repetitive B2 (Alu-like) sequences in rat liver following hepatocarcinogen exposure. Cell Growth Differ. 7(5):635-46.

Rats were treated with low doses of the hepatocarcinogens dimethylnitrosamine or thioacetamide, and livers were examined 48 h later. These treatments are known to produce altered RNA compartmentation, wherein a class of repetitive RNA sequences normally restricted to the nucleus appears in the cytoplasm. Reverse transcription-PCR amplifications demonstrated that the sequences showing altered compartmentation consisted largely of a subfamily of the rodent B2 sequence family, the counterpart of human Alu sequences involved in retrotransposition. Northern blot analyses showed that these B2 sequences were found in cytoplasmic RNA as 170- to 360- nucleotide "sense" transcripts, and competition hybridization experiments established that B2 sequences represented most (if not all) of the sequences showing altered compartmentation. The major increase in B2 transcriptions in cytoplasmic RNA was not associated with any change in B2 transcription by RNA polymerase III. In situ hybridizations showed that the altered compartmentation of B2 sequences occurred in well-delineated foci within the rat liver; these foci consisted of a central region containing a prominent infiltrate of macrophages admixed with small hepatocytes and a peripheral region of histologically normal hepatocytes that showed evidence of oxidative damage. Altered compartmentation of B2 sequences may represent an important focal initiatory change in a subset of hepatocytes, whereas subsequent retrotranspositional events (associated with Alu-like sequences) could predispose initiated cell foci to alterations in promotion/progression phases.

Englander, E. W., and B. H. Howard. 1996. A naturally occurring T14A11 tract blocks nucleosome formation over the human neurofibromatosis type 1 (NF1)-Alu element. J Biol Chem. 271(10):5819-23.

The nature of chromatin organization over Alu repetitive elements is of interest with respect to the maintenance of their transcriptional silencing as well as their potential to influence local chromatin structure. We previously demonstrated that the pattern of nucleosomal organization over Alu elements in native chromatin is specific and similar to the pattern observed with an in vitro reconstituted Alu template. This pattern, distinguished by a nucleosome centered over the 5 -end of the Alu element, is associated with repression of polymerase III-dependent transcription in vitro (Englander, E. W., Wolffe, A. P., and Howard, B. H. (1993) J. Biol. Chem. 268, 19565-19573; Englander, E. W., and Howard, B. H. (1995) J. Biol. Chem. 270, 10091-10096). In the current study, additional templates representing both evolutionarily old and young Alu subfamilies were found to direct a similar pattern of nucleosome assembly, consistent with the view that nucleosome positioning in vitro is shared by a majority of Alus. We discovered however, that the specific nucleosome positioning pattern was disrupted over one member of a young Alu subfamily, which recently transposed immediately downstream to a T14A11 sequence in the neurofibromatosis type 1 locus (Wallace, M. R., Andersen, L. B., Saulino, A. M., Gregory, P. E., Glover, T. W., and Collins, F. S. (1991) Nature 353, 864-866). Upon removal of this sequence motif, the expected pattern of assembly was restored to the neurofibromatosis type 1-Alu template. This finding indicates that, at least in vitro, certain sequences can override the propensity for positioning nucleosomes that is inherent to Alu elements. The finding also raises the possibility that a similar situation may occur in vivo, with potential implications for understanding mechanisms by which certain Alu elements may evade chromatin-mediated transcriptional silencing.

Flint, J., J. Rochette, C. F. Craddock, C. Dode, B. Vignes, S. W. Horsley, L. Kearney, V. J. Buckle, H. Ayyub, and D. R. Higgs. 1996. Chromosomal stabilisation by a subtelomeric rearrangement involving two closely related Alu elements. Hum Mol Genet. 5(8):1163-9.

We have characterised a subtelomeric rearrangement involving the short arm of chromosome 16 that gives rise to alpha-thalassaemia by deleting the major, remote regulatory element controlling alpha-globin expression. The chromosomal breakpoint lies in an Alu family repeat located only approximately 105 kb from the 16p subtelomeric region. The broken chromosome has been stabilised with a newly positioned telomere acquired by recombination between this 16p Alu element and a closely related subtelomeric Alu element of the Sx subfamily. It seems most likely that this abnormal chromosome has been rescued by the mechanism of telomere capture which may reflect a more general process by which subtelomeric sequences are normally dispersed between chromosomal ends.

Hofferbert, S., J. Muller, H. Kostering, W. D. von Ohlen, and M. Schloesser. 1996. A novel 5'-upstream mutation in the factor XII gene is associated with a TaqI restriction site in an Alu repeat in factor XII-deficient patients. Hum Genet. 97(6):838-41.

The factor XII gene from factor XII-deficient patients was screened for mutations at the genomic level. In patients negative for cross-reacting material, a T to C transition 224 bp upstream of exon 3 was identified (exon 3-224 (T --> C)) that creates an additional TaqI restriction site in intron B. This mutation is located within a putative hormone responsive element and within a B box promoter of an Alu repeat of the Sb0 family. The TaqI site is associated with a G to C transversion upstream of the transcription initiation site (exon 1-8 (G --> C)). We discuss the possible roles of these elements in factor XII gene regulation.

Humphrey, G. W., E. W. Englander, and B. H. Howard. 1996. Specific binding sites for a pol III transcriptional repressor and pol II transcription factor YY1 within the internucleosomal spacer region in primate Alu repetitive elements. Gene Expr. 6(3):151-68.

Alu interspersed repetitive elements possess internal RNA polymerase III promoters that are transcribed in vitro and in transfected mouse cells but are nearly silent in human HeLa cells. Transcriptional repression of these elements is to some extent reversible, as pol III- dependent Alu expression can be induced with herpes simplex or adenovirus. To assess whether sequence-specific DNA binding proteins might contribute to Alu transcriptional silencing, we examined the internucleosomal spacer region surrounding the B box of the Alu pol III promoter in HeLa cell nuclei for evidence of proteins bound at specific sites in vivo. We identified a DNase I-hypersensitive site 5' to the B box and a DNase I-resistant region 3' to the B box in nuclei. An Alu- specific repressor binds to a 5-bp inverted repeat motif overlapping the 5' end of the TFIIIC binding site and may inhibit pol III transcription through competitive displacement. The level of Alu- specific pol III repressor activity is significantly reduced in adenovirus-infected HeLa cells, suggesting that the repressor may contribute to Alu transcriptional silencing in vivo. The 3' DNase I- resistant region coincided with a binding site for the pol II transcription factor YY1 in vitro. YY1 is one of the major proteins in HeLa cells having binding specificity for Alu elements. YY1 bound to tandem arrays of genomic Alu elements may play a role in chromatin organization and silencing.

Jarnik, M., J. Q. Tang, M. Korab-Laskowska, E. Zietkiewicz, G. Cardinal, I. Gorska-Flipot, D. Sinnett, and D. Labuda. 1996. Overall informativity, OI, in DNA polymorphisms revealed by inter-Alu PCR: detection of genomic rearrangements. Genomics. 36(3):388-98.

We studied two systems of multilocus markers revealed by PCR using primers directing amplification between Alu repeats in a tail-to-tail orientation. Genomic polymorphisms were detected as the presence or absence of the electrophoretic bands representing DNA fragments of a given length. A total of 104 such fragments segregating as Mendelian markers in a panel of eight CEPH families were analyzed by two-point linkage analysis. Fifty-one of these fragments were localized with respect to CEPH markers; they represented 33 loci, 7 of which were multiallelic. Locus-specific oligonucleotides were developed and used as hybridization probes to identify the mapped loci within a complex pattern of inter-Alu PCR products. A great proportion of inter-Alu PCR polymorphisms represented length variants within amplified DNA segments, while others were presumably due to mutations within the priming sites. To describe the expected number of informative loci per typing experiment we introduced a parameter called overall informativity (OI), which provides a single measure of the multiplex ratio and the informativity of markers contributing to a multilocus system (OI of a single locus is equivalent to its heterozygosity and cannot exceed 0.5 for a biallelic codominant marker). High OI values (5.8 and 11.5) of the two presented systems of inter-Alu PCR markers of random chromosomal distribution render them suitable for mapping genomic rearrangements such as genomic deletions in tumoral tissues. This was illustrated by the detection of loss of heterozygosity in the 9q22-qter region in sporadic colon cancer.

Kapitonov, V., and J. Jurka. 1996. The age of Alu subfamilies. J Mol Evol. 42(1):59-65.

Using Kimura's distance measure we have calculated the average age of all major Alu subfamilies based on the most recent available data. We conclude that AluJ sequences are some 26 Myr older than previously thought. Furthermore, the origin of the FLA (Free Left Arm) Alu family can be traced back to the very beginning of the mammalian radiation. One new minor subfamily is reported and discussed in the context of sequence diversity in major Alu subfamilies.

Kazakov, V. I., M. P. Svetlova, V. P. Boiko, R. I. Krutilina, V. V. Zenin, N. D. Aksenov, A. N. Shatrova, V. M. Bozhkov, and N. V. Tomilin. 1996. [The physical mapping of human chromosomes. II. The production of unique chromosome-specific DNA fragments using the polymerase chain reaction with oligonucleotide primers to conservative regions of Alu repeats]. Tsitologiia. 38(4-5):510-6.

Unique DNA fragments localised between Alu-repeats have been produced by PCR. The reaction was carried out with oligonucleotide primers to conservative regions of Alu-repeats. The DNA fragments from different pulls, individual clones, chromosome-specific clonotecs derived from phage lambda, cosmids and individual human chromosomes served as matrixes. The possibilities are discussed of Alu-primer applying in production of exceptional physical features of DNA molecules, suitable for constructing clone couple groups and for direct physical mapping on the DNA of isolated chromosomes, missing the stage of cloning.

Kazakov, V. I., and N. V. Tomilin. 1996. Increased concentration of some transcription factor binding sites in human retroposons of the Alu family. Genetica. 97(1):15-22.

Eukaryotic gene expression is dependent on short protein-binding DNA sequence motifs promoting the assembly of multiprotein transcription complexes. Human retroposons of the Alu family are known to contain some high-affinity binding sites for transcription factors, which may serve as signals in regulation of expression of RNA-polymerase II- transcribed genes. In this computer study we have compared the density of ten consensus transcription factor binding sites in a set of human mature mRNA, human promotors and Alu repeats. Our results indicate that Alu retroposons and promotor sequences have significantly higher mean density of these sites compared to RNAs. It is suggested that the majority of Alu repeats do have the potential for regulating gene expression via modulation of RNA polymerase II-dependent transcription.

Knight, A., M. A. Batzer, M. Stoneking, H. K. Tiwari, W. D. Scheer, R. J. Herrera, and P. L. Deininger. 1996. DNA sequences of Alu elements indicate a recent replacement of the human autosomal genetic complement. Proc Natl Acad Sci U S A. 93(9):4360-4.

DNA sequences of neutral nuclear autosomal loci, compared across diverse human populations, provide a previously untapped perspective into the mode and tempo of the emergence of modern humans and a critical comparison with published clonally inherited mitochondrial DNA and Y chromosome measurements of human diversity. We obtained over 55 kilobases of sequence from three autosomal loci encompassing Alu repeats for representatives of diverse human populations as well as orthologous sequences for other hominoid species at one of these loci. Nucleotide diversity was exceedingly low. Most individuals and populations were identical. Only a single nucleotide difference distinguished presumed ancestral alleles from descendants. These results differ from those expected if alleles from divergent archaic populations were maintained through multiregional continuity. The observed virtual lack of sequence polymorphism is the signature of a recent single origin for modern humans, with general replacement of archaic populations.

Konstantinova, I. M., V. A. Kulichkova, O. A. Petukhova, I. V. Kozhukharova, L. V. Turoverova, I. V. Volkova, O. R. Il'kaeva, B. Ermolaeva Iu, L. V. Teslenko, A. G. Mittenberg, L. N. Ignatova, and L. N. Gauze. 1996. [A novel class of small RNP (alpha-RNP) in human cell line K-562 and coordinated control of expression of Alu-containing messenger RNA]. Dokl Akad Nauk. 350(2):268-71.

Krajinovic, M., C. Richer, D. Labuda, and D. Sinnett. 1996. Detection of a mutator phenotype in cancer cells by inter-Alu polymerase chain reaction. Cancer Res. 56(12):2733-7.

A mutator phenotype due to a DNA mismatch repair deficiency is usually detected by typing a number of microsatellite markets. Here, eight hereditary nonpolyposis colon cancer patients with microsatellite instability were investigated by inter-Alu PCR, known to amplify DNA segments that may represent preferential targets of replication errors. Among 40-60 bands revealed in a single PCR experiment, more than 20% were found altered in tumoral DNA samples compared to matched normal samples from the same patient. Shifts and changes in signal intensity accounted for most of the alterations, whereas gains or losses of bands were rare. Certain bands were affected only in a single patient, whereas the instabilities in others were common. These results suggest that some genomic regions are more susceptible than others to the expression of a mutator phenotype. Four such bands altered in at least five patients were characterized further and shown to be unstable because of contractions of the Alu poly(A) tails. Interestingly, none of the bands representing loci shown previously to be polymorphic in the population displayed instability in the tumoral samples. Inter-Alu PCR appears to be a robust, cost-effective, and sensitive technique for revealing the mutator phenotype in cancer cells.

Kropotov, A. V., and N. V. Tomilin. 1996. Evidence for a regulatory protein complex on RNA polymerase III promoter of human retroposons of Alu family. Genetica. 98(3):223-33.

Abundant human retroposons of the Alu family produce few RNA polymerase III (RPIII)-dependent transcripts in vivo. This suggests that either the bulk of the repeats has no proper promoter elements or that transcription of Alu by RPIII is repressed. In this study, we analyzed complexes formed by human nuclear proteins with the Alu B-box and with an adjacent downstream sequence (DB-sequence). Four complexes (C1-C4) were detected and two of them (C2 and C3) were found to be induced by different proteins. C3 formation was found to be sensitive to minor sequence variation within the Alu DB-sequence. The C2 complex is specifically repressed by the competing VA1 B-box oligonucleotide and was found to be very stable. In addition, it is downregulated in human cells transformed by adenovirus 5. This is consistent with a view that the C2 complex is formed by a protein (designated as ACR1) that is different from TFIIIC2. The ACR1 protein may be involved in the modulation of Alu transcription in vivo by interfering or cooperating with TFIIIC2. A similar complex is detected with the efficiently transcribed adenovirus VA1 RNA gene B-box. We compared the affinity of complexes formed by ACR1 with Alu and VA1 B-boxes. It was found that both B-boxes bind ACR1 with equal affinity with a dissociation constant of about 2 nM. However, DB-sequences in Alu and VA1 promoters are non- homologous, and C3/C4 complexes are found to be formed with Alu DB, but not formed with VA1 DB sequences. The Alu-specific protein forming C3 (named as ACR2) may cooperate with ACR1 in selective repression of RPIII-dependent Alu transcription in vivo.

Marshall, B., G. Isidro, and M. G. Boavida. 1996. Insertion of a short Alu sequence into the hMSH2 gene following a double cross over next to sequences with chi homology [published erratum appears in Gene 1997 Sep 15;197(1-2):413]. Gene. 174(1):175-9.

Alu repeat sequences and other multiple copy repetitive elements are present throughout the human genome and are active in promoting recombination. It is believed that reverse transcription of transcribed Alu repeats followed by chromosomal integration has been responsible for the wide dispersion and high copy number of these sequences. During studies on the hMSH2 gene we have used RT-PCR to amplify from peripheral blood lymphocytes a cDNA species in which 553 base pairs of hMSH2 cDNA have been deleted to be replaced by a short 36 base pair Alu sequence as a result of a genomic insertion/deletion event. The 36 base pair Alu insert is homologous to a 26 base pair Alu sequence previously implicated in the promotion of recombination and contains the GCTGG motif which is part of the prokaryotic chi sequence. A second chi-like sequence is also located within the deleted hMSH2 region. Both chi-like sequences are located within 4 bp of the two 4-bp regions of cross over containing the insertion/deletion breakpoints. This suggest that a double recombination event has occurred, providing direct evidence for the recombinogenic activity of this Alu element. Furthermore, it suggests that chi-like sequences may define recombination hotspots as in prokaryotes.

Mauillon, J. L., P. Michel, J. M. Limacher, J. B. Latouche, P. Dechelotte, F. Charbonnier, C. Martin, V. Moreau, J. Metayer, B. Paillot, and T. Frebourg. 1996. Identification of novel germline hMLH1 mutations including a 22 kb Alu- mediated deletion in patients with familial colorectal cancer. Cancer Res. 56(24):5728-33.

We analyzed the hMLH1 gene in 17 unrelated families with putative hereditary nonpolyposis colorectal cancer. The complete hMLH1 cDNA was amplified in one step, and after a second amplification, four overlapping segments were directly sequenced. We detected, in five families that did not meet the complete Amsterdam criteria, five alterations, including a double-base change resulting in a missense mutation (Lys-618-Ala), a splicing mutation affecting the intron 4 splice acceptor site, a 2-bp deletion at codon 726, a 7-bp deletion at codon 626, and a deletion of exons 13-16. The latter alteration was shown to result from a 22-kb genomic deletion due to a homologous recombination between Alu repeats located in introns 12 and 16. The detection of five germline hMLH1 mutations in five families that only partially fulfilled the Amsterdam criteria shows that these criteria do not allow the identification of all familial colorectal cancers due to mutations of the mismatch repair genes. The numerous Alu repeats present within the hMLH1 gene and the observation of large genomic deletions suggest that (a) Alu-mediated deletions might frequently be involved in hMLH1 inactivation, and (b) reverse transcription-PCR analysis, which allows the amplification of the entire coding region of the hMLH1 gene in one step, might be the most appropriate method for the detection of hMLH1 alterations.

Milewicz, D. M., P. H. Byers, J. Reveille, A. L. Hughes, and M. Duvic. 1996. A dimorphic Alu Sb-like insertion in COL3A1 is ethnic-specific. J Mol Evol. 42(2):117-23.

Alu elements are a class of repetitive DNA sequences found throughout the human genome that are thought to be duplicated via an RNA intermediate in a process termed retroposition. Recently inserted Alu elements are closely related, suggesting that they are derived from a single source gene or closely related source genes. Analysis of the type III collagen gene (COL3A1) revealed a polymorphic Alu insertion in intron 8 of the gene. The Alu insertion in the COL3A1 gene had a high degree of nucleotide identity to the Sb family of Alu elements, a family of older Alu elements. The Alu sequence was less similar to the consensus sequence for the PV or Sb2 subfamilies, subfamilies of recently inserted Alu elements. These data support the observations that at least three source genes are active in the human genome, one of which is distinct from the PV and Sb2 subfamilies and predates either of these two subfamilies. Appearance of the Alu insertion in different ethnic populations suggests that the insertion may have occurred in the last 100,000 years. This Alu insert should be a useful marker for population studies and for marking COL3A1 alleles.

Piedrafita, F. J., R. B. Molander, G. Vansant, E. A. Orlova, M. Pfahl, and W. F. Reynolds. 1996. An Alu element in the myeloperoxidase promoter contains a composite SP1- thyroid hormone-retinoic acid response element. J Biol Chem. 271(24):14412-20.

An Alu element preceding the myeloperoxidase gene (MPO) contains four hexamer motifs related to the consensus recognition sequence for nuclear hormone receptors (AGGTCA), arranged as direct repeats with spacing of 2, 4, and 2 nucleotides (DR-2-4-2). Gel shift experiments and transient transfection assays demonstrate that these sequences include binding sites for retinoic acid and thyroid hormone receptors and function in vivo to activate transcription of a chloramphenicol acetyltransferase reporter gene. The first DR-2 elements of the series do not bind known receptors but do bind the SP1 transcription factor. Two alleles of the MPO gene exist that differ at one position within this element, resulting in one allele with and one without a strong SP1 binding site. The element with the SP1 site activates transcription by 25-fold in transient transfection assays, while the alternative allele confers severalfold less transcriptional activity. Most cases of acute myelocytic leukemia are homozygous for the allele with the SP1 binding site, suggesting this element plays an important role in regulating the MPO gene in myeloid leukemias. This MPO-Alu is a representative of an Alu subclass numbering approximately 400,000 copies, suggesting many genes may be regulated by such elements.

Schmid, C. W. 1996. Alu: structure, origin, evolution, significance and function of one- tenth of human DNA. Prog Nucleic Acid Res Mol Biol. 53:283-319.

Shaikh, T. H., and P. L. Deininger. 1996. The role and amplification of the HS Alu subfamily founder gene. J Mol Evol. 42(1):15-21.

A recently identified Alu element (Leeflang et al. J. Mol. Evol. 1993, 37:559-565), referred to as the "putative founder of the HS (PV) subfamily," was found to be present at orthologous loci in the human, chimpanzee, gorilla, and gibbon lineages. The evolution of this Alu suggested that it is a source gene in the evolution of Alu family repeats for one of the most recent subfamilies, HS. We have determined that this putative founder of the HS subfamily was not present at the orthologous loci in older primates, including old world and new world monkeys. Thus, this particular Alu locus has only been responsible for the establishment of a very small subfamily of Alu sequences. We have further demonstrated that this putative founder Alu was not responsible for the de novo Alu insertion into the neurofibromatosis-1 gene of an individual causing neurofibromatosis. Our data demonstrate that although the putative founder of the HS subfamily found by Leeflang et al. (1993) probably gave rise to one of the most recent subfamilies of Alu sequences, it has not been very active in retroposition.

Tishkoff, S. A., G. Ruano, J. R. Kidd, and K. K. Kidd. 1996. Distribution and frequency of a polymorphic Alu insertion at the plasminogen activator locus in humans. Hum Genet. 97(6):759-64.

We have investigated the frequency distribution, across a broad range of geographically dispersed populations, of alleles of the polymorphic Alu insertion that occurs within the 8th intron of the tissue plasminogen, activator gene (PLAT). This Alu is a member of a recently derived subfamily of Alu elements that has been expanding during human evolution and continues to be transpositionally active. We used a "population tube" approach to screen 10 chromosomes from each of 19 human populations for presence or absence of this Alu in the PLAT locus and found that all tested populations are dimorphic for presence/absence of this insertion. We show that the previously published EcoRI, HincII, PstI, TaqI, and XmnI polymorphisms at the PLAT locus all result from insertion of this Alu and we use both restriction fragment length polymorphism and polymerase chain reaction analysis to examine the frequency of Alu(+) and Alu(-) alleles in a sample of 1003 individuals from 27 human populations and in 38 nonhuman primates. Nonhuman primates are monomorphic for the Alu(-) allele. Human populations differ substantially in allele frequency, and in several populations both alleles are common. Our results date the insertion event prior to the spread and diversification of modern humans.

Tombran-Tink, J., K. Mazuruk, I. R. Rodriguez, D. Chung, T. Linker, E. Englander, and G. J. Chader. 1996. Organization, evolutionary conservation, expression and unusual Alu density of the human gene for pigment epithelium-derived factor, a unique neurotrophic serpin. Mol Vis. 2:11.

PEDF is a neurotrophic serpin that promotes a neuronal phenotype and augments neuronal cell survival. The isolation, sequence and structural analysis of the human PEDF gene and its promoter along with its evolutionary conservation and expression in human tissues are now described. The gene spans approximately 16 kb and is divided among 8 exons and 7 introns, the junctions of which conform to the AG/GT consensus rule. PEDF appears to fall into the ovalbumin/PAI-2 subgrouping of serpins and is structurally far different from GDN/PN-1, the only other neurotrophic serpin reported to date. The immediate 5'- flanking region is dominated by a dense cluster of Alu repeats in which are embedded several promoter consensus sequences. A CAAT box is present at -43. The putative promoter region is also far different from that reported for GDN/PN-1. Comparable hybridization signals of 23 kb EcoRI fragments containing the PEDF gene are observed by Southern blot analysis in all primate, mammal and avian species examined; conservation is particularly evident among the primates. Northern blot analysis confirms the presence of the PEDF transcript in a broad range of human fetal and adult tissues including almost all brain areas examined, underscoring differences with GDN/PN-1 which, in the adult brain, is only expressed in glia and a subset of neurons.

Yamagata, H., T. Miki, M. Nakagawa, K. Johnson, R. Deka, and T. Ogihara. 1996. Association of CTG repeats and the 1-kb Alu insertion/deletion polymorphism at the myotonin protein kinase gene in the Japanese population suggests a common Eurasian origin of the myotonic dystrophy mutation. Hum Genet. 97(2):145-7.

We have studied linkage disequilibrium between CTG repeats and an Alu insertion/deletion polymorphism at the myotonin protein kinase gene (DMPK) in 102 Japanese families, of which 93 were affected with myotonic dystrophy (DM). All of the affected chromosomes are in complete linkage disequilibrium with the Alu insertion allele. Among the normal chromosomes, alleles of CTG repeats 5 and > or = 17 are exclusively associated with the insertion allele. On the other hand, intermediate alleles of 11-16 repeats show a significantly greater association with the deletion allele. A strikingly similar pattern of linkage disequilibrium observed in European populations suggests a common origin of the DM mutation in the Japanese and European populations.

Yang, A. S., M. L. Gonzalgo, J. M. Zingg, R. P. Millar, J. D. Buckley, and P. A. Jones. 1996. The rate of CpG mutation in Alu repetitive elements within the p53 tumor suppressor gene in the primate germline. J Mol Biol. 258(2):240-50.

Cytosine to thymine transition mutations at the CpG dinucleotide are the most common point mutations in cancer and genetic disease. We calculated the in vivo rate of CpG mutation in the primate germline by deriving a primordial consensus sequence for an Alu repetitive element which inserted into intron 6 of the primate p53 gene 35 to 55 million years ago. Comparison of this primordial sequence to the Alu sequence in intron 6 of present-day primates was used to determine the nature and rate of mutations which occurred during evolution. We estimate the half-life of a CpG nucleotide to be 24 to 60 million years, and the rate constant for mutation at this dinucleotide to be 1.2 x 1O(-8) to 2.9 x 1O(-8) years(-1). These results were confirmed by the analysis of a second Alu sequence in intron 10 of the p53 gene. The in vivo mutation rate is at least 1250-fold slower than the in vitro chemical rate of 5-methylcytosine deamination in double-stranded DNA, showing that current estimates of CpG mutation repair have been significantly underestimated. Furthermore, the mutability of the CpG dinucleotide has led to the depletion of this dinucleotide from the vertebrate genome, and calculations in this study suggest that current levels of the CpG dinucleotide in the primate genome are very close to a steady state equilibrium in which the rate of CpG mutation is equal to the rate of CpG formation by random mutation.

Arcot, S. S., A. W. Adamson, J. E. Lamerdin, B. Kanagy, P. L. Deininger, A. V. Carrano, and M. A. Batzer. 1996. Alu fossil relics--distribution and insertion polymorphism [letter]. Genome Res. 6(11):1084-92.

Screening of a human genomic library with an oligonucleotide probe specific for one of the young subfamilies of Alu repeats (Ya5/8) resulted in the identification of several hundred positive clones. Thirty-three of these clones were analyzed in detail by DNA sequencing. Oligonucleotide primers complementary to the unique sequence regions flanking each Alu repeat were used in PCR-based assays to perform phylogenetic analyses, chromosomal localization, and insertion polymorphism analyses within different human population groups. All 33 Alu repeats were present only in humans and absent from orthologous positions in several nonhuman primate genomes. Seven Alu repeats were polymorphic for their presence/absence in three different human population groups, making them novel identical-by-descent markers for the analysis of human genetic diversity and evolution. Nucleotide sequence analysis of the polymorphic Alu repeats showed an extremely low nucleotide diversity compared with the subfamily consensus sequence with an average age of 1.63 million years old. The young Alu insertions do not appear to accumulate preferentially on any individual human chromosome.

Arcot, S. S., Z. Wang, J. L. Weber, P. L. Deininger, and M. A. Batzer. 1995. Alu repeats: a source for the genesis of primate microsatellites. Genomics. 29(1):136-44.

As a result of their abundance, relatively uniform distribution, and high degree of polymorphism, microsatellites and minisatellites have become valuable tools in genetic mapping, forensic identity testing, and population studies. In recent years, a number of microsatellite repeats have been found to be associated with Alu interspersed repeated DNA elements. The association of an Alu element with a microsatellite repeat could result from the integration of an Alu element within a preexisting microsatellite repeat. Alternatively, Alu elements could have a direct role in the origin of microsatellite repeats. Errors introduced during reverse transcription of the primary transcript derived from an Alu "master" gene or the accumulation of random mutations in the middle A-rich regions and oligo(dA)-rich tails of Alu elements after insertion and subsequent expansion and contraction of these sequences could result in the genesis of a microsatellite repeat. We have tested these hypotheses by a direct evolutionary comparison of the sequences of some recent Alu elements that are found only in humans and are absent from nonhuman primates, as well as some older Alu elements that are present at orthologous positions in a number of nonhuman primates. The origin of "young" Alu insertions, absence of sequences that resemble microsatellite repeats at the orthologous loci in chimpanzees, and the gradual expansion of microsatellite repeats in some old Alu repeats at orthologous positions within the genomes of a number of nonhuman primates suggest that Alu elements are a source for the genesis of primate microsatellite repeats.

Batzer, M. A., C. M. Rubin, U. Hellmann-Blumberg, M. Alegria-Hartman, E. P. Leeflang, J. D. Stern, H. A. Bazan, T. H. Shaikh, P. L. Deininger, and C. W. Schmid. 1995. Dispersion and insertion polymorphism in two small subfamilies of recently amplified human Alu repeats. J Mol Biol. 247(3):418-27.

Newly isolated members of two recently propagated (young) Alu subfamilies were examined for sequence diversity and insertion polymorphism in primate genomes. The smaller subfamily (termed HS-2) is comprised of approximately 5 to 25 members, while the larger (termed Sb2) includes approximately 125 to 600 members. Individual members of these Alu subfamilies share distinguishing sets of diagnostic mutations, are well-conserved relative to each other, and have expanded in the human lineage. At least one member from each subfamily is known to be polymorphic in humans. Three newly characterized HS-2 Alu family members as well as three Sb2 Alu repeats are monomorphic (fixed) in humans. The existence of a number of Alu subfamilies that have amplified in parallel within the human genome provides compelling evidence for the simultaneous activity of multiple dispersed Alu source genes.

Benlian, P., J. Etienne, J. L. de Gennes, L. Noe, D. Brault, A. Raisonnier, F. Arnault, J. Hamelin, L. Foubert, J. C. Chuat, and et al. 1995. Homozygous deletion of exon 9 causes lipoprotein lipase deficiency: possible intron-Alu recombination. J Lipid Res. 36(2):356-66.

We studied a homozygous deletion in the lipoprotein lipase gene at the molecular level. Comprising the end of intron 8, the whole of exon 9, and about two-thirds of intron 9, this 2.136-kb deletion caused complete lipoprotein lipase deficiency and severe hypertriglyceridemia (type I hyperlipoproteinemia). Intron 9 of a normal control subject was also sequenced in order to define the exact borders of the deletion. Up to now, only the first 0.721 kb of intron 9 had been sequenced. Thus the complete sequence of intron 9 (3.090 kb) is now available. Three Alu sequences were characterized in the normal intron 9, while the proband had only the third complete Alu sequence. The first Alu sequence was located in the deleted region, and only the left arm of the second was present, as the deletion began near its center. A stem- loop structure involving a 14-nt region towards the end of intron 8 and an Alu sequence in intron 9 might have led to the deletion. Sequence analysis showed that the three Alu sequences belonged to the 40-million- year-old Alu-Sa subclass.

Chang, D. Y., N. Sasaki-Tozawa, L. K. Green, and R. J. Maraia. 1995. A trinucleotide repeat-associated increase in the level of Alu RNA- binding protein occurred during the same period as the major Alu amplification that accompanied anthropoid evolution. Mol Cell Biol. 15(4):2109-16.

Nearly 1 million Alu elements in human DNA were inserted by an RNA- mediated retroposition-amplification process that clearly decelerated about 30 million years ago. Since then, Alu sequences have proliferated at a lower rate, including within the human genome, in which Alu mobility continues to generate genetic variability. Initially derived from 7SL RNA of the signal recognition particle (SRP), Alu became a dominant retroposon while retaining secondary structures found in 7SL RNA. We previously identified a human Alu RNA-binding protein as a homolog of the 14-kDa Alu-specific protein of SRP and have shown that its expression is associated with accumulation of 3'-processed Alu RNA. Here, we show that in early anthropoids, the gene encoding SRP14 Alu RNA-binding protein was duplicated and that SRP14-homologous sequences currently reside on different human chromosomes. In anthropoids, the active SRP14 gene acquired a GCA trinucleotide repeat in its 3'-coding region that produces SRP14 polypeptides with extended C-terminal tails. A C-->G substitution in this region converted the mouse sequence CCA GCA to GCA GCA in prosimians, which presumably predisposed this locus to GCA expansion in anthropoids and provides a model for other triplet expansions. Moreover, the presence of the trinucleotide repeat in SRP14 DNA and the corresponding C-terminal tail in SRP14 are associated with a significant increase in SRP14 polypeptide and Alu RNA-binding activity. These genetic events occurred during the period in which an acceleration in Alu retroposition was followed by a sharp deceleration, suggesting that Alu repeats coevolved with C-terminal variants of SRP14 in higher primates.

Chesnokov, I. N., and C. W. Schmid. 1995. Specific Alu binding protein from human sperm chromatin prevents DNA methylation. J Biol Chem. 270(31):18539-42.

A protein from human sperm nuclei that specifically binds to Alu DNA repeats has been purified. The specific DNA binding site of this protein within the Alu sequence has been mapped by methylation interference and electrophoretic mobility shift assays. This sperm Alu binding protein selectively protects Alu elements from methylation in vitro and may be responsible for the unmethylated state of Alu sequences in the male germ line resulting in a parent-specific differential inheritance of Alu methylation.

Chu, W. M., W. M. Liu, and C. W. Schmid. 1995. RNA polymerase III promoter and terminator elements affect Alu RNA expression. Nucleic Acids Res. 23(10):1750-7.

Promoter elements derived from the 7SL RNA gene stimulate RNA polymerase III (Pol III) directed Alu transcription in vitro. These elements also stimulate expression of Alus transfected into 293 cells, but transcripts from these same constructs are undetectable in HeLa cells. A terminator resembling the terminator for the 7SL RNA gene has no effect on in vitro Alu template activity, but increases expression in vivo in a position independent manner. Alu transcripts generated from templates with and without this terminator have identical half- lives, indicating that this terminator stimulates expression by increasing template activity. Together, these results show that Alu expression may be regulated at multiple levels and can respond to cis- acting elements. This new found ability to express Alu transcripts by transient transfection provides an opportunity to monitor their post- transcriptional fate. Primary Alu transcripts are not extensively adenylated or deadenylated following transcription, but are short-lived compared to 118 nt scAlu RNA. In addition to Alu RNA, transfected templates encode scAlu RNA, but very high levels of Alu RNA expression does not increase the abundance of scAluRNA. ScAluRNA is not merely a transient RNA degradation product, but is instead tightly regulated by factors other than the abundance of primary transcripts.

Englander, E. W., and B. H. Howard. 1995. Nucleosome positioning by human Alu elements in chromatin. J Biol Chem. 270(17):10091-6.

Alu sequences are interspersed throughout the genomes of primate cells, occurring singly and in clusters around RNA polymerase II-transcribed genes. Because these repeat elements are capable of positioning nucleosomes in in vitro reconstitutes (Englander, E. W., Wolffe, A. P., and Howard, B. H. (1993) J. Biol. Chem. 268, 19565-19573), we investigated whether they also influence in vivo chromatin structure. When assayed collectively using consensus sequence probes and native chromatin as template, Alu family members were found to confer rotational positioning on nucleosomes or nucleosome-like particles. In particular, a 10-base pair pattern of DNase I nicking that spanned the RNA polymerase III box A promoter motif extended upstream to cover diverse 5'-flanking sequences, suggesting that Alu repeats may influence patterns of nucleosome formation over neighboring regions. Computational analysis of a set of naturally occurring Alu sequences indicated that nucleosome positioning information is intrinsic to these elements. Inasmuch as local chromatin organization influences gene expression, the capacity of Alu sequences to affect chromatin structure as demonstrated here may help to clarify some features of these elements.

Hanke, J. H., J. E. Hambor, and P. Kavathas. 1995. Repetitive Alu elements form a cruciform structure that regulates the function of the human CD8 alpha T cell-specific enhancer. J Mol Biol. 246(1):63-73.

We previously identified a T cell-specific enhancer in the last intron of the human CD8 alpha gene that is adjacent to a sequence element that significantly represses enhancer function. This negative regulatory region consists of a half-Alu sequence that has potential to base-pair with a downstream Alu element, which is part of the fully active enhancer, to form a cruciform structure. The activity of this half-Alu silencer sequence is position and orientation-dependent, suggesting that DNA structure plays an important role in its function. Using site- directed mutational analysis and P1 nuclease mapping, we directly demonstrate that formation of a cruciform structure is required for repression of enhancer function in transient transfection assays. Finally, a P1 nuclease-sensitive site is present in the endogenous CD8 alpha gene in T cell lines providing indirect evidence that the stem- loop may form in vivo. Taken together, these results suggest that Alu elements may contribute to the regulation of the CD8 alpha gene enhancer through the formation of secondary structure that disrupts enhancer function.

Hewitt, S. M., G. C. Fraizer, and G. F. Saunders. 1995. Transcriptional silencer of the Wilms' tumor gene WT1 contains an Alu repeat. J Biol Chem. 270(30):17908-12.

Expression of the Wilms' tumor gene WT1 is tightly regulated throughout development. In contrast, the WT1 promoter is promiscuous, functioning in all cell lines tested. We have cloned a transcriptional silencer that is involved in regulation of the WT1 gene. The transcriptional silencer is located in the third intron of the WT1 gene, approximately 12 kilobases from the promoter, and functions to repress transcription from the WT1 promoter in cell lines of non-renal origin. The 460-base pair silencer region is unusual in that it contains a full-length Alu repeat. We have also cloned an enhancer like-element located 1.3 kilobases upstream of the WT1 promoter.

Hsu, K., D. Y. Chang, and R. J. Maraia. 1995. Human signal recognition particle (SRP) Alu-associated protein also binds Alu interspersed repeat sequence RNAs. Characterization of human SRP9. J Biol Chem. 270(17):10179-86.

Nearly 1 million interspersed Alu elements reside in the human genome. Alu retrotransposition is presumably mediated by full-length Alu transcripts synthesized by RNA polymerase III, while some polymerase III-synthesized Alu transcripts undergo 3'-processing and accumulate as small cytoplasmic (sc) RNAs of unknown function. Interspersed Alu sequences also reside in the untranslated regions of some mRNAs. The Alu sequence is related to a portion of the 7SL RNA component of signal recognition particle (SRP). This region of 7SL RNA together with 9- and 14-kDa polypeptides (SRP9/14) regulates translational elongation of ribosomes engaged by SRP. Here we characterize human (h) SRP9 and show that it, together with hSRP14 (SRP9/14), forms the activity previously identified as Alu RNA-binding protein (RBP). The primate-specific C- terminal tail of hSRP14 does not appreciably affect binding to scAlu RNA. Kd values for three Alu-homologous scRNAs were determined using Alu RBP (SRP9/14) purified from HeLa cells. The Alu region of 7SL, scAlu, and scB1 RNAs exhibited Kd values of 203 pM, 318 pM, and 1.8 nM, respectively. Finally, Alu RBP can bind with high affinity to synthetic mRNAs that contain interspersed Alus in their untranslated regions.

Janicic, N., Z. Pausova, D. E. Cole, and G. N. Hendy. 1995. Insertion of an Alu sequence in the Ca(2+)-sensing receptor gene in familial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism. Am J Hum Genet. 56(4):880-6.

Missense mutations in the calcium-sensing receptor (CaR) gene have previously been identified in patients with familial hypocalciuric hypercalcemia (FHH) and neonatal severe hyperparathyroidism (NSHPT). We studied family members of a Nova Scotian deme expressing both FHH and NSHPT and found, by PCR amplification of CaR gene exons, that FHH individuals were heterozygous and NSHPT individuals were homozygous for an abnormally large exon 7. This is due to an insertion at codon 877 of an Alu-repetitive element of the predicted-variant/human-specific-1 subfamily. It is in the opposite orientation to the CaR gene and contains an exceptionally long poly(A) tract. Stop signals are introduced in all reading frames within the Alu sequence, leading to a predicted shortened mutant CaR protein. The loss of the majority of the CaR carboxyl-terminal intracellular domain would dramatically impair its signal transduction capability. Identification of the specific mutation responsible for the FHH/NSHPT phenotype in this community will allow rapid testing of at-risk individuals.

Knebelmann, B., L. Forestier, L. Drouot, S. Quinones, C. Chuet, F. Benessy, J. Saus, and C. Antignac. 1995. Splice-mediated insertion of an Alu sequence in the COL4A3 mRNA causing autosomal recessive Alport syndrome. Hum Mol Genet. 4(4):675-9.

Alport syndrome is a mainly X-linked hereditary disease of basement membranes characterized by progressive renal failure, deafness, and ocular lesions. The alpha 3(IV) and alpha 4(IV) collagen genes have been recently shown to be involved in the less frequent autosomal recessive form. When screening lymphocyte COL4A3 mRNAs from Alport patients, we found a mutant whose transcripts were disrupted by a 74 bp insertion at the junction of exons IV or V and VI. The insertion derives from an antisense Alu element in COL4A3 intron V, which has been spliced into the alpha 3(IV) mRNA due to a G to T transversion activating a cryptic acceptor splice site in this Alu element. There is complete segregation of this mutation with the disease in the family. Our findings provide the first evidence for the pathogenic role of abnormal splicing of COL4A3. Moreover, we demonstrate the superiority of mutation screening at the mRNA level to detect a hitherto poorly recognized mutation mechanism in humans, splice-mediated insertion of an Alu fragment into a coding sequence.

Kochanek, S., D. Renz, and W. Doerfler. 1995. Transcriptional silencing of human Alu sequences and inhibition of protein binding in the box B regulatory elements by 5'-CG-3' methylation. FEBS Lett. 360(2):115-20.

In earlier work, we demonstrated that 5'-CG-3' methylation inhibits the transcriptional activity of human Alu elements associated with the alpha 1-globin and the angiogenin genes in a cell-free transcription system from HeLa nuclear extracts. These studies have been extended to different Alu sequences and to investigations on the mechanism involved in transcriptional silencing by methylation. By comparing the results of DNase I and dimethyl sulfate (DMS) in vitro footprinting on a consensus sequence in the RNA polymerase III promoter control B region between the unmethylated and the 5'-CG-3' methylated B box, evidence has been adduced for effects of 5'-CG-3' methylation on the interaction of specific nuclear proteins with DNA sequences in the B control region of the Alu elements. These results are consistent with the interpretation that the 5'-CG-3' methylation interferes with the binding of proteins that are essential for the function of the B control region in these RNA polymerase III-transcribed elements, and that promoter methylation thus inhibits transcription.

McHaffie, G. S., and S. H. Ralston. 1995. Origin of a negative calcium response element in an ALU-repeat: implications for regulation of gene expression by extracellular calcium. Bone. 17(1):11-4.

The negative calcium response element type 2 (nCARE) is a regulatory DNA sequence consisting of a palindromic core sequence and several upstream T residues, which was originally described in the 5' flank of the human PTH gene. The nCARE functions in an orientation-specific manner to inhibit PTH transcription in response to raised extracellular calcium levels. Here we report that the PTH nCARE lies within a hitherto unrecognized ALU-like element situated approximately 3.6 kB upstream of the human PTH gene transcriptional start site. Since ALU elements are repetitive DNA sequences, which are widely distributed throughout the human genome, we hypothesized that other nCARE elements might also exist. A search of the GenBank/EMBL databases with the nCARE core sequence confirmed this to be the case showing the presence of 111 copies of the nCARE in human/primate sequences. Analysis of the 7SL RNA sequence from which ALU elements derive also showed the presence of an nCARE "core" sequence immediately upstream of the poly-A+ tail. These data suggest that the nCARE is derived from retrotransposition of 7SL RNA and forms an integral part of many ALU elements; reverse transcription of the poly-A+ tail of 7SL RNA adds T residues, which on retrotransposition into genomic DNA with the core sequence, forms an ALU element containing a functional nCARE. Some of the genes associated with nCARE elements express products which are affected by extracellular calcium concentrations and work is in progress to determine the functional effects of nCARE at these sites.(ABSTRACT TRUNCATED AT 250 WORDS)

Meese, E., H. W. Muller, N. Brass, J. M. Trent, and N. Blin. 1995. Assignment of Alu-repetitive sequences to large restriction fragments from human chromosomes 6 and 22. Mol Biol Rep. 21(2):81-4.

We have employed a pulsed field gel electrophoresis and Alu hybridization approach for identification of large restriction fragments on chromosome 6 and 22. This technique allows large portions of selected human chromosomes to be visualized as discrete hybridization signals. Somatic cell hybrid DNA which contains chromosome 6 or chromosome 22 was restricted with either Notl or Mlul. The restriction fragments were separated by pulsed field gel electrophoresis (PFGE) and hybridized against an Alu repetitive sequence (Blur 8). The hybridization signals result in a fingerprint- like pattern which is unique for each chromosome and each restriction enzyme. In addition, a continuous pattern of restriction fragments was demonstrated by gradually increasing puls times. This approach will also be suitable to analyze aberrant human chromosomes retained in somatic cell hybrids and can be used to analyze flow sorted human chromosomes. To this end, our method provides a valuable alternative to standard cytogenetic analysis.

Mullersman, J. E., and L. M. Pfeffer. 1995. An Alu cassette in the cytoplasmic domain of an interferon receptor subunit. J Interferon Cytokine Res. 15(9):815-7.

All the cloned subunits of interferon receptors (IFNRs) belong to the type II cytokine receptor family (CRF2). Although three members of CRF2 encoded on human chromosome 21 share a 50 amino acid cytoplasmic homology domain (the IRH2 domain), a fourth subunit, the second cloned chain of the type I IFNR (IFNIR-2), contains a juxtamembrane 20 amino acid stretch of high similarity to the IRH2 domain that stops abruptly. Comparison of the membrane-distal portion of the IFNIR-2 cytoplasmic domain with sequence databases revealed a very high similarity to Alu repeat sequences. We provide evidence that all but 18 amino acids of the predicted cytoplasmic domain of the IFNIR-2 chain are encoded by an Alu cassette in its antisense orientation. Incorporation of an Alu cassette into the receptor chain is proposed to occur by a splicing mechanism. All previous well-characterized examples of insertion of an antisense Alu cassette into an open reading frame have involved alternative splicing. Thus, we predict the existence of an alternatively spliced product of the IFNIR-2 chain with a substantially different cytoplasmic domain.

Norris, J., D. Fan, C. Aleman, J. R. Marks, P. A. Futreal, R. W. Wiseman, J. D. Iglehart, P. L. Deininger, and D. P. McDonnell. 1995. Identification of a new subclass of Alu DNA repeats which can function as estrogen receptor-dependent transcriptional enhancers. J Biol Chem. 270(39):22777-82.

We have utilized a genetic selection system in yeast to identify novel estrogen-responsive genes within the human genome and to define the sequences in the BRCA-1 gene responsible for its estrogen responsiveness. This approach led to the identification of a new subclass within the Alu family of DNA repeats which have diverged from known Alu sequences and have acquired the ability to function as estrogen receptor-dependent enhancers. Importantly, these new elements confer receptor-dependent estrogen responsiveness to a heterologous promoter when assayed in mammalian cells. This transcriptional activity can be attenuated by the addition of either of three different classes of estrogen receptor antagonists, indicating that these elements function as classical estrogen receptor-dependent enhancers. Furthermore, this enhancer activity is restricted to a specific subset of DNA repeats because consensus Alu elements of four major subfamilies do not respond to the estrogen receptor. Previously, most Alu sequences have been considered to be functionally inert. However, this work provides strong evidence that a significant subset can confer estrogen responsiveness upon a promoter within which they are located. Clearly, Alu sequences must now be considered as important contributors to the regulation of gene transcription in estrogen receptor-containing cells.

Panning, B., and J. R. Smiley. 1995. Activation of expression of multiple subfamilies of human Alu elements by adenovirus type 5 and herpes simplex virus type 1. J Mol Biol. 248(3):513-24.

The nearly one million Alu repetitive elements in the human genome can be grouped into a number of subfamilies. Comparisons between subfamily consensus sequences suggest that Alu evolution is characterized by the sequential amplification and dispersal of a limited number of Alu founder sequences. The S, Sb and Sb1 subfamilies provide an example of such a related series of Alu subfamilies. We have previously demonstrated that adenovirus type 5 and herpes simplex virus type 1 activate RNA polymerase III transcription of endogenous Alu elements in HeLa cells. Here, we report that expression of Alu sequences belonging to the S, Sb and Sb1 subfamilies was activated following infection with these viruses. The data indicate that transpositionally inactive Alu elements can give rise to high levels of pol III transcripts in the presence of appropriate trans-acting factors and demonstrate that the class III promoters of a significant number and variety of Alu sequences are functional in vivo. Multiple subfamilies of Alu sequences were induced in transformed and non-transformed cell types, suggesting that induction of Alu expression may be part of the normal cellular response to viral infection.

Rudiger, N. S., N. Gregersen, and M. C. Kielland-Brandt. 1995. One short well conserved region of Alu-sequences is involved in human gene rearrangements and has homology with prokaryotic chi. Nucleic Acids Res. 23(2):256-60.

Alu elements have repeatedly been found involved in gene rearrangements in humans. Although these elements have been suggested to stimulate gene rearrangements, sparse information is available for the possible mechanism(s) of these events. Here we present a compilation of Alu elements that have been involved in recombinational events leading to gene rearrangements, indicating the presence of a common 26 bp core sequence at or close to the sites of recombination. Besides the obvious possibility of retrotransposition, gene rearrangements may be induced by sequences that stimulate genetic recombination. We suggest that the core sequence stimulates recombination and may thereby cause the frequent involvement of these elements in gene rearrangements. Curiously, the core sequence contains the pentanucleotide motif CCAGC, which is also part of chi, an 8 bp sequence known to stimulate recBC mediated recombination in Escherichia coli.

Russanova, V. R., C. T. Driscoll, and B. H. Howard. 1995. Adenovirus type 2 preferentially stimulates polymerase III transcription of Alu elements by relieving repression: a potential role for chromatin. Mol Cell Biol. 15(8):4282-90.

The number of Alu transcripts that accumulate in HeLa and other human cells is normally very low; however, infection with adenovirus type 5 increases the expression of Alu elements dramatically, indicating that the potential for polymerase III (pol III)-dependent Alu transcription in vivo is far greater than generally observed (B. Panning and J.R. Smiley, Mol. Cell. Biol. 13:3231-3244, 1993). In this study, we employed nuclear run-on in combination with a novel RNase H-based assay to investigate transcription from uninfected and adenovirus type 2- infected nuclei, as well as genomic DNAs from uninfected and infected cells. When performed in the presence of excess uninfected nuclear extract, such assays revealed that (i) the vast majority of transcriptionally competent Alu elements in nuclei are masked from the pol III transcriptional machinery and (ii) the induction of Alu expression upon adenovirus infection can be largely accounted for by an increased availability of these elements to the pol III transcription machinery. We also investigated the role of H1 histone for silencing of Alu genes and, in comparison, mouse B2 repetitive elements. Depletion of H1 led to an approximately 17-fold activation of B2 repetitive elements but did not change Alu transcription relative to that of constitutively expressed 5S rRNA genes. These results are consistent with the view that Alu repeats are efficiently sequestered by chromatin proteins, that such masking cannot be accounted for by nonspecific H1- dependent repression, and that adenovirus infection at least partially overrides the repressive mechanism(s).

Shiraishi, M., and T. Sekiya. 1995. Mutations in an Alu repeated sequence associated with the DXS43 locus in human small cell lung cancers. Oncogene. 10(7):1453-4.

Point mutations in an Alu repeated sequence associated with the DXS43 locus were identified in two out of 10 human small cell lung cancers. Since these aberrations were identified in DNA from both metastatic lesions and primary lesions from the same patient, they would appear to have occurred at a relatively early stage. Although this sequence is not apparently associated with known genes, these tumor-specific mutations occurred at an early stage may play an important role in tumorigenesis.

Vansant, G., and W. F. Reynolds. 1995. The consensus sequence of a major Alu subfamily contains a functional retinoic acid response element. Proc Natl Acad Sci U S A. 92(18):8229-33.

Alu repeats are interspersed repetitive DNA elements specific to primates that are present in 500,000 to 1 million copies. We show here that an Alu sequence encodes functional binding sites for retinoic acid receptors, which are members of the nuclear receptor family of transcription factors. The consensus sequences for the evolutionarily recent Alu subclasses contain three hexamer half sites, related to the consensus AGGTCA, arranged as direct repeats with a spacing of 2 bp, which is consistent with the binding specificities of retinoic acid receptors. An analysis was made of the DNA binding and transactivation potential of these sites from an Alu sequence that has been previously implicated in the regulation of the keratin K18 gene. These Alu double half sites are shown to bind bacterially synthesized retinoic acid receptors as assayed by electrophoretic mobility shift assays. These sites are further shown to function as a retinoic acid response element in transiently transfected CV-1 cells, increasing transcription of a reporter gene by a factor of approximately 35-fold. This transactivation requires cotransfection with vectors expressing retinoic acid receptors, as well as the presence of all-trans-retinoic acid, which is consistent with the known function of retinoic acid receptors as ligand-inducible transcription factors. The random insertion of potentially thousands of Alu repeats containing retinoic acid response elements throughout the primate genome is likely to have altered the expression of numerous genes, thereby contributing to evolutionary potential.

Yulug, I. G., A. Yulug, and E. M. Fisher. 1995. The frequency and position of Alu repeats in cDNAs, as determined by database searching. Genomics. 27(3):544-8.

The Alu repeat sequence is estimated to account for 5% of human genomic DNA. The precise relationship of Alu sequences to human fully spliced cDNA has yet to be determined, although many new protocols for cloning cDNAs either depend on the presence of Alus or--more usually--rely on their absence in a population of messages. Previous estimates of the percentage of fully spliced human transcripts that contain Alu repeats have relied on hybridization procedures. Here we have gone directly to the DNA sequence by extracting over 1600 entries from GenBank that are described as human complete cDNAs, and we have assessed the frequency with which the Alu repeat sequence occurs in these sequences. We find that 5% of fully spliced human cDNAs contain Alu sequences. In addition, we have quantified the appearance of Alus in the different cDNA regions, 5' untranslated region (UTR), coding region, and 3' UTR. The vast majority of Alus are found in the 3' UTR, but 14% lie in the 5' UTR, and very rarely an Alu sequence is present within, or partially within, the coding region of the transcript.

Arcot, S. S., J. J. Fontius, P. L. Deininger, and M. A. Batzer. 1995. Identification and analysis of a 'young' polymorphic Alu element. Biochim Biophys Acta. 1263(1):99-102.

A polymorphic Alu element belonging to a young subfamily of Alu repeats has been identified. Sequence analysis showed that this Alu element is flanked by perfect direct repeats and a 3' oligo(dA)-rich tail. The Alu element, designated A25, is deleted by 34 nucleotides at the 5' end and has a single CpG mutation compared to the human-specific consensus sequence. Using a PCR-based assay, we demonstrated that the A25 Alu repeat is localized to human chromosome 8 and is polymorphic in humans.

Arranz, V., M. Kress, and M. Ernoult-Lange. 1994. The gene encoding the MOK-2 zinc-finger protein: characterization of its promoter and negative regulation by mouse Alu type-2 repetitive elements. Gene. 149(2):293-8.

The mouse gene MOK-2 encodes a protein with seven highly similar zinc fingers. The MOK-2 transcripts are preferentially detected in transformed cell lines, brain and testis tissues. The characterized 5'- flanking sequence differs from those of tissue-specific genes previously described. DNA sequence analysis shows that the promoter region lacks TATA and CCAAT boxes. Two short interspersed mouse genomic repeats (B2 sequences) found in this region exert a negative cis-acting effect on MOK-2 promoter activity.

Baldini, A., and E. A. Lindsay. 1994. Mapping human YAC clones by fluorescence in situ hybridization using Alu-PCR from single yeast colonies. Methods Mol Biol. 33:75-84.

Batzer, M. A., M. Alegria-Hartman, and P. L. Deininger. 1994. A consensus Alu repeat probe for physical mapping. Genet Anal Tech Appl. 11(2):34-8.

Physical mapping of the human genome involves a variety of complex hybridization-based procedures, some of which rely upon the ability to separate human clones derived from human-rodent hybrid cell lines from those that contain background rodent-derived DNA sequences. The ability to block the repetitive element (Alu repeat) portion of inter-Alu PCR products derived from a variety of complex sources is also crucial for the isolation of unique DNA sequences. Here we report the construction and characterization of a new consensus Alu repeat probe (pPD39) designed for these purposes.

Batzer, M. A., M. Stoneking, M. Alegria-Hartman, H. Bazan, D. H. Kass, T. H. Shaikh, G. E. Novick, P. A. Ioannou, W. D. Scheer, R. J. Herrera, and et al. 1994. African origin of human-specific polymorphic Alu insertions. Proc Natl Acad Sci U S A. 91(25):12288-92.

Alu elements are a family of interspersed repeats that have mobilized throughout primate genomes by retroposition from a few "master" genes. Among the 500,000 Alu elements in the human genome are members of the human-specific subfamily that are not fixed in the human species; that is, not all chromosomes carry an Alu element at a particular locus. Four such polymorphic human-specific Alu insertions were analyzed by a rapid, PCR-based assay that uses primers that flank the insertion point to determine genotypes based on the presence or absence of the Alu element. These four polymorphic Alu insertions were shown to be absent from the genomes of a number of nonhuman primates, consistent with their arising as human genetic polymorphisms sometime after the human/African ape divergence. Analysis of 664 unrelated individuals from 16 population groups from around the world revealed substantial levels of variation within population groups and significant genetic differentiation among groups. No significant associations were found among the four loci, consistent with their location on different chromosomes. A maximum-likelihood tree of population relationships showed four major groupings consisting of Africa, Europe, Asia/Americas, and Australia/New Guinea, which is concordant with similar trees based on other loci. A particularly useful feature of the polymorphic Alu insertions is that the ancestral state is known to be the absence of the Alu element, and the presence of the Alu element at a particular chromosomal site reflects a single, unique event in human evolution. A hypothetical ancestral group can then be included in the tree analysis, with the frequency of each insertion set to zero. The ancestral group connected to the maximum-likelihood tree within the African branch, which suggests an African origin of these polymorphic Alu insertions. These data are concordant with other diverse data sets, which lends further support to the recent African origin hypothesis for modern humans. Polymorphic Alu insertions represent a source of genetic variation for studying human population structure and evolution.

Britten, R. J. 1994. Evidence that most human Alu sequences were inserted in a process that ceased about 30 million years ago. Proc Natl Acad Sci U S A. 91(13):6148-50.

The primate Alu interspersed repeats can be subdivided into classes on the basis of shared nucleotides at a set of diagnostic positions. Each of the classes of Alu sequences is apparently the result of past retrotransposition of transcripts of highly conserved class-specific source genes that differed from each other at the diagnostic positions. The nucleotides at the majority of positions are identical among the source genes and therefore were identical among all of the Alu sequences at the time of their insertion. These CONSBI (conserved before insertion) positions are useful because the changes that have occurred after insertion are recognizable and the divergence resulting from nucleotide substitutions, insertions, and deletions is informative. The divergence of Alu sequences at the CONSBI positions is a measure of the time since a class was inserted. The greatest majority of Alu sequences are in one class (identified as class II), and it is particularly suitable for such examination, since nearly full-length sequences are now known for nearly a thousand members of this class. The average divergence of class II members indicates that the class has an average age of about 40 million years. The distribution in divergence of class II accurately fits a sum of two Poisson distributions. The implication is that class II Alu sequences were derived from two massive past events of insertion of many Alu sequences. In this model the younger subset of class II sequences (corresponding to about 300,000 copies in the genome) has an average divergence of 5% at CONSBI positions. The older set of class II sequences (corresponding to about 150,000 genomic copies) has a 9% average divergence. Based on the drift rate of primate DNA sequences, the events of insertion probably occurred 30-50 million years ago. The goodness of the fit to the Poisson distribution indicates that no significant number of members of class II have been inserted since 30 million years ago.

Britten, R. J. 1994. Evolutionary selection against change in many Alu repeat sequences interspersed through primate genomes. Proc Natl Acad Sci U S A. 91(13):5992-6.

Mutations have been examined in the 1500 interspersed Alu repeats of human DNA that have been sequenced and are nearly full length. There is a set of particular changes at certain positions that rarely occur (termed suppressed changes) compared to the average of identical changes of identical nucleotides in the rest of the sequence. The suppressed changes occur in positions that are clustered together in what appear to be sites for protein binding. There is a good correlation of the suppression in different positions, and therefore the joint probability of absence of mutation at many pairs of such positions is significantly higher than that expected at random. The suppression of mutation appears to result from selection that is not due to requirements for Alu sequence replication. The implication is that hundreds of thousands of Alu sequences have sequence-dependent functions in the genome that are selectively important for primates. In a few known cases Alu inserts have been adapted to function in the regulation of gene transcription.

Brookfield, J. F. 1994. The human Alu SINE sequences--is there a role for selection in their evolution? Bioessays. 16(11):793-5.

The Alu sequence is a SINE (Short INterspersed Element) that is abundant in the human genome. A new analysis (1) reveals an unexpected conservation of some bases in the DNA sequence of the element. The bases involved include those forming an RNA polymerase III promoter. An unresolved question is whether this conservation results from selection for transposability. This, in turn, is related to the larger question of the evolutionary relationship between members of the Alu sequence family.

Chang, D. Y., B. Nelson, T. Bilyeu, K. Hsu, G. J. Darlington, and R. J. Maraia. 1994. A human Alu RNA-binding protein whose expression is associated with accumulation of small cytoplasmic Alu RNA. Mol Cell Biol. 14(6):3949-59.

Human Alu sequences are short interspersed DNA elements which have been greatly amplified by retrotransposition. Although initially derived from the 7SL RNA component of signal recognition particle (SRP), the Alu sequence has evolved into a dominant transposon while retaining a specific secondary structure found in 7SL RNA. We previously characterized a set of Alu sequences which are expressed as small cytoplasmic RNAs and isolated a protein that binds to these transcripts. Here we report that biochemical purification of this protein revealed it as the human homolog of the SRP 14 polypeptide which binds the Alu-homologous region of 7SL RNA. The human cDNA predicts an alanine-rich C-terminal tail translated from a trinucleotide repeat not found in the rodent homolog, which accounts for why the human protein-RNA complex migrates more slowly than its rodent counterpart in RNA mobility shift assays. The human Alu RNA- binding protein (RBP) is expressed after transfection of this cDNA into mouse cells. Expression of human RBP in rodent x human somatic cell hybrids is associated with substantial increase in endogenous small cytoplasmic Alu and scB1 transcripts but not other small RNAs. These studies provide evidence that this RBP associates with Alu transcripts in vivo and affects their metabolism and suggests a role for Alu transcripts in translation in an SRP-like manner. Analysis of hybrid lines indicated that the Alu RBP gene maps to human chromosome 15q22, which was confirmed by Southern blotting. The possibility that the primate-specific structure of this protein may have contributed to Alu evolution is considered.

Claverie, J. M., and W. Makalowski. 1994. Alu alert [letter]. Nature. 371(6500):752.

de Souza, A. P., V. Allamand, I. Richard, L. Brenguier, I. Chumakov, D. Cohen, and J. S. Beckmann. 1994. Targeted development of microsatellite markers from inter-Alu amplification of YAC clones. Genomics. 19(2):391-3.

Primary genetic maps based on highly informative markers are now available. The local density of these markers may, however, not be sufficient. There is thus a need for new means to generate polymorphic markers from targeted regions of the genome. This can be achieved by selectively cloning and sequencing (CA)n-positive human inter-Alu sequences from targeted YAC clones. This method was tested on 21 YACs and led to the development of seven new polymorphic microsatellite markers.

Gambari, R., S. Volinia, C. Nesti, C. Scapoli, and I. Barrai. 1994. A set of Alu-free frequent decamers from mammalian genomes enriched in transcription factor signals. Comput Appl Biosci. 10(5):501-8.

We have recently reported that the statistical analysis of the frequency distribution of short oligonucleotides within mammalian and viral genomes allows the production of sets of DNA sequences enriched in signals for transcription factors. Such statistical approaches could facilitate the identification of new promoter regions playing a role in the transcriptional regulation of gene expression. In the case of mammalian oligonucleotides, we found that the published set of frequent decamers enriched in transcriptional motifs is not suitable for studies on genes of Homo sapiens and evolutionarily related genomes, because it contains decameric sequences belonging to genomic repeats. We report here that most of the decameric sequences of DNA repeats belong to Alu repeats. Accordingly, we produced a subset of Alu-free frequent decamers. In addition, we eliminated from the subset of Alu-free frequent decamers those that are frequently present within other common human repeats, including (GT)n, (AT)n, (CA)n, (ATT)n, (CAA)n and (GTT)n. The Alu-free (repeats-free) subset of frequent mammalian decamers is enriched in signals for transcription factors and allows the identification of putative signals in genes, such as those coding for plasminogen activator, adenosine deaminase and p53, that contain a large number of Alu-like repeats interspersed within our genomic sequences. The newly generated compilation of frequent decamers described here might be used to locate genomic regions playing functional roles in the expression of genes of Homo sapiens and related primates.

Gosden, J., M. Breen, and D. Lawson. 1994. Alu- and L1-primed PCR-generated probes for nonisotopic in situ hybridization. Methods Mol Biol. 29:479-92.

Hammer, M. F. 1994. A recent insertion of an alu element on the Y chromosome is a useful marker for human population studies. Mol Biol Evol. 11(5):749-61.

A member of the Alu family of repeated DNA elements has been identified on the long arm of the human Y chromosome, Yq11. This element, referred to as the Y Alu polymorphic (YAP) element, is present at a specific site on the Y chromosome in some humans and is absent in others. Phylogenetic comparisons with other Alu sequences reveal that the YAP element is a member of the polymorphic subfamily-3 (PSF-3), a previously undefined subfamily of Alu elements. The evolutionary relationships of PSF-3 to other Alu subfamilies support the hypothesis that recently inserted elements result from multiple source genes. The frequency of the YAP element is described in 340 individuals from 14 populations, and the data are combined with those from other populations. There is both significant heterogeneity among populations and a clear pattern in the frequencies of the insertion: sub-Saharan Africans have the highest frequencies, followed by northern Africans, Europeans, Oceanians, and Asians. An interesting exception is the relatively high frequency of the YAP element in Japanese. The greatest genetic distance is observed between the African and non-African populations. The YAP is especially useful for studying human population history from the perspective of male lineages.

He, X. P., N. Bataille, and H. M. Fried. 1994. Nuclear export of signal recognition particle RNA is a facilitated process that involves the Alu sequence domain. J Cell Sci. 107(Pt 4):903-12.

The signal recognition particle is a cytoplasmic RNA-protein complex that mediates translocation of secretory polypeptides into the endoplasmic reticulum. We have used a Xenopus oocyte microinjection assay to determine how signal recognition particle (SRP) RNA is exported from the nucleus. Following nuclear injection, SRP RNA accumulated in the cytoplasm while cytoplasmically injected SRP RNA did not enter the nucleus. Cytoplasmic accumulation of SRP RNA was an apparently facilitated process dependent on limiting trans-acting factors, since nuclear export exhibited saturation kinetics and was completely blocked either at low temperature or by wheat germ agglutinin, a known inhibitor of nuclear pore-mediated transport. At least one target for trans-acting factors that promote nuclear export of SRP RNA appears to be the Alu element of the molecule, since a transcript consisting of only the Alu sequence was exported from the nucleus in a temperature-dependent manner and the Alu transcript competed in the nucleus for transport with intact SRP RNA. Although the identities of trans-acting factors responsible for SRP RNA transport are at present unknown, we suggest that proteins contained within the cytoplasmic form of SRP are candidates. Consistent with this idea were the effects of a mutation in SRP RNA that prevented binding of two known SRP proteins to the Alu sequence.

Heikkinen, J., T. Hautala, K. I. Kivirikko, and R. Myllyla. 1994. Structure and expression of the human lysyl hydroxylase gene (PLOD): introns 9 and 16 contain Alu sequences at the sites of recombination in Ehlers-Danlos syndrome type VI patients. Genomics. 24(3):464-71.

Lysyl hydroxylase (EC 1.14.11.4) catalyzes the formation of hydroxylysine in collagens by the hydroxylation of lysine residues in peptide linkages. This enzyme activity is known to be reduced in patients with the type VI variant of the Ehlers-Danlos syndrome, and the first mutations in the lysyl hydroxylase gene (PLOD) have recently been identified. We have now isolated genomic clones for human lysyl hydroxylase and determined the complete structure of the gene, which contains 19 exons and a 5' flanking region with characteristics shared by housekeeping genes. The constitutive expression of the gene in different tissues further suggests that lysyl hydroxylase has an essential function. We have sequenced the introns of the gene in the region where many mutations and rearrangements analyzed to date are concentrated. Intron 9 and intron 16 show extensive homology resulting from the many Alu sequences found in these introns. Intron 9 contains five and intron 16 eight Alu sequences. The high homology and many short identical or complementary sequences in these introns generate many potential recombination sites with the gene. The delineation of the structure of the lysyl hydroxylase gene contributes significantly to our understanding of the rearrangements in the genome of Ehlers- Danlos type VI patients.

Hoefler, G., M. Forstner, M. C. McGuinness, W. Hulla, M. Hiden, P. Krisper, L. Kenner, T. Ried, C. Lengauer, R. Zechner, and et al. 1994. cDNA cloning of the human peroxisomal enoyl-CoA hydratase: 3- hydroxyacyl-CoA dehydrogenase bifunctional enzyme and localization to chromosome 3q26.3-3q28: a free left Alu Arm is inserted in the 3' noncoding region. Genomics. 19(1):60-7.

Enoyl-CoA hydratase:3-hydroxyacyl-CoA dehydrogenase bifunctional enzyme is one of the four enzymes of the peroxisomal beta-oxidation pathway. Here, we report the full-length human cDNA sequence and the localization of the corresponding gene on chromosome 3q26.3-3q28. The cDNA sequence spans 3779 nucleotides with an open reading frame of 2169 nucleotides. The tripeptide SKL at the carboxy terminus, known to serve as a peroxisomal targeting signal, is present. DNA sequence comparison of the coding region showed an 80% homology between human and rat bifunctional enzyme cDNA. The 3' noncoding sequence contains 117 nucleotides homologous to an Alu repeat. Based on sequence comparison, we propose that these nucleotides are a free left Alu arm with 86% homology to the Alu-J family. RNA analysis shows one band with highest intensity in liver and kidney. This cDNA will allow in-depth studies of molecular defects in patients with defective peroxisomal bifunctional enzyme. Moreover, it will also provide a means for studying the regulation of peroxisomal beta-oxidation in humans.

Iizuka, M., C. Jones, K. Hayashi, and T. Sekiya. 1994. Mapping of 28 (CA)n microsatellite repeats and 13 Alu markers on human chromosome 11 using a panel of somatic cell hybrids. Genomics. 19(3):581-4.

Kass, D. H., C. Aleman, M. A. Batzer, and P. L. Deininger. 1994. Identification of a human specific Alu insertion in the factor XIIIB gene. Genetica. 94(1):1-8.

The factor XIIIB gene was examined to determine the nature of a previously described 300 bp restriction fragment length polymorphism (RFLP) seen in the human population. Polymerase chain reaction analysis of different regions within the factor XIIIB gene was carried out to define a high resolution map of the region encompassing the polymorphism, followed by DNA sequence analysis. An Alu insertion was found to be the source of this variation. This Alu repeat is a member of the human specific-1 (HS-1) subfamily, although one of the five diagnostic nucleotides is a cattarhine specific (CS) subfamily mutation, suggesting that it may represent an intermediate form in the evolution between these two subfamilies. Subsequently, we developed a PCR-based assay to detect the polymorphism, rendering it a more useful marker for genetic linkage studies and genome mapping. This insertion is also a valuable polymorphism for human population studies, as demonstrated by the large variations in allele frequencies seen in three population groups.

Kobets, N. D., R. G. Borissov, E. L. Chernolovskaya, V. V. Gorn, and V. V. Vlassov. 1994. Oligo(A), oligo(TG), and Alu repeats of DNA in chromatin are available for sequence-specific chemical modification with oligodeoxynucleotide derivatives. Antisense Res Dev. 4(4):259-62.

Reaction of 4-(N-2-chloroethyl-N-methylamino) benzylphosphamides of oligonucleotides, which are targeted to the poly(A), poly(TG), and Alu repeats of eukaryotic DNA in chromatin and isolated nuclei from HeLa cells, has been investigated. It was found that the reagents alkylate DNA and some proteins due to specific complex formation. The affinity character of the reaction was proved by the fact that free corresponding oligonucleotides taken in excess or preliminary treatment of chromatin with S1 nuclease both prevent the biopolymers from the modification. Deproteinated DNA from the same cells does not react with oligonucleotide derivatives. This suggests that the chromatin DNA must have some structural features allowing oligonucleotide binding. Reactivity may be attributed to the existence of strongly negative supercoiled DNA regions containing single-stranded sequences or regions where DNA can unwind in the presence of complementary oligonucleotides. Results obtained suggest that in eukaryotic chromatin there are open DNA sequences available for affinity modification with oligonucleotide derivatives not only due to formation of triple helixes.

Liu, W. M., R. J. Maraia, C. M. Rubin, and C. W. Schmid. 1994. Alu transcripts: cytoplasmic localisation and regulation by DNA methylation. Nucleic Acids Res. 22(6):1087-95.

Full length Alu transcripts in HeLa cells are detected by primer extension using reverse transcriptase and are also analyzed as cloned cDNA sequences. The 5' end of these transcripts corresponds to the transcriptional start site for RNA polymerase III indicating that these RNAs are transcribed from their internal polymerase III promoters. The Alu transcripts found in cytoplasmic poly A+ RNAs appear to be organized into RNPs as assayed by sucrose gradient sedimentation. Present at about one hundred to one thousand copies per cell, the Alu transcripts are rare as compared to 7SL RNA. In agreement with previous reports that methylation inhibits Pol III-directed transcription of Alu in vitro, treatment of HeLa cells with 5-azacytidine results in Alu DNA hypomethylation and an increase in the abundance of the Alu transcript. Sequence analysis shows that many different Alu repeats including members of all subfamilies are transcribed by Pol III in vivo. cDNA sequences of the Pol III-directed transcripts exactly match the A box of the Pol III promoter element whereas in other Alu transcripts this element is not faithfully conserved.

Makalowski, W., G. A. Mitchell, and D. Labuda. 1994. Alu sequences in the coding regions of mRNA: a source of protein variability. Trends Genet. 10(6):188-93.

Dispersion of repetitive sequence elements is a source of genetic variability that contributes to genome evolution. Alu elements, the most common dispersed repeats in the human genome, can cause genetic diseases by several mechanisms, including de novo Alu insertions and splicing of intragenic Alu elements into mRNA. Such mutations might contribute positively to protein evolution if they are advantageous or neutral. To test this hypothesis, we searched the literature and sequence databases for examples of protein-coding regions that contain Alu sequences: 17 Alu 'cassettes' inserted within 15 different coding sequences were found. In three instances, these events caused genetic diseases; the possible functional significance of the other Alu- containing mRNAs is discussed. Our analysis suggests that splice- mediated insertion of intronic elements is the major mechanism by which Alu segments are introduced into mRNAs.

Margalit, H., E. Nadir, and S. A. Ben-Sasson. 1994. A complete Alu element within the coding sequence of a central gene [letter]. Cell. 78(2):173-4.

Mnukova-Fajdelova, M., Y. Satta, C. O'HUigin, W. E. Mayer, F. Figueroa, and J. Klein. 1994. Alu elements of the primate major histocompatibility complex. Mamm Genome. 5(7):405-15.

The chromosomal region constituting the major histocompatibility complex (MHC) has undergone complex evolution that is often difficult to decipher. An important aid in the elucidation of the MHC evolution is the presence of Alu elements (repeats) which serve as markers for tracing chromosomal rearrangements. As the first step toward the establishment of sets of evolutionary markers for the MHC, Alu elements present in selected MHC haplotypes of the human species, the gorilla, and the chimpanzee were identified. Restriction fragments of cosmid clones from the libraries of the three species were hybridized with Alu- specific probes, Alu elements were amplified by the polymerase chain reaction, and the amplification products were sequenced. In some cases, sequences of the regions flanking the Alu elements were also obtained. Altogether, 31 new Alu elements were identified, representing six Alu subfamilies. The average density of Alu elements in the MHC is one element per four kilobases (kb) of sequence. Alu elements have apparently been inserted steadily into the MHC over the last 65 million years (my). On average, one Alu element is inserted into the primate MHC every 4 my. Analysis of the human DR3 haplotype supports its origin by duplication from an ancestral haplotype consisting of DRB1 and DRB2 genes. The sharing of an old Alu element by the DRB1 and DRB2 genes, in turn, supports their divergence from a common ancestor more than 55 my ago.

Mullenbach, R., S. Tisborn, and N. Blin. 1994. Sequence patterns and hybridization analysis of clones generated by Alu- PCR. DNA Seq. 4(4):249-52.

A series of clones from an Alu-PCR library were analysed in more detail. Characterization by Southern blot hybridization and sequencing displayed several features common to all probes generated by this approach: Short length of the PCR-products as well as the presence of homologous regions on both ends resulted in a limited feasibility for filter hybridization and a low probability of restriction length polymorphisms. In addition, a series of different short repeats at the 3'-ends of Alu-repeats and present in the generated probes offers a rich source of potential variable sites accessible by PCR.

Panning, B., and J. R. Smiley. 1994. Activation of RNA polymerase III transcription of human Alu elements by herpes simplex virus. Virology. 202(1):408-17.

We found that HSV infection of HeLa cells strongly induces RNA polymerase III transcription of endogenous human Alu elements, resulting in the accumulation of high levels of cytoplasmic RNAs initiated from Alu pol III promoters. Induction required viral protein synthesis and occurred during infection with a viral mutant bearing a null mutation in the immediate-early (IE) gene encoding ICP4, suggesting that one or more IE proteins are sufficient for activation. However, mutations in each of the other four IE genes had no effect on activation of Alu expression. We therefore conclude that HSV most likely encodes at least two proteins that are each sufficient to activate Alu transcription and that at least one of these is an IE protein other than ICP4.

Pousi, B., T. Hautala, J. Heikkinen, L. Pajunen, K. I. Kivirikko, and R. Myllyla. 1994. Alu-Alu recombination results in a duplication of seven exons in the lysyl hydroxylase gene in a patient with the type VI variant of Ehlers- Danlos syndrome. Am J Hum Genet. 55(5):899-906.

The type VI variant of the Ehlers-Danlos syndrome (EDS) is a recessively inherited connective-tissue disorder. The characteristic features of the variant are muscular hypotonia, kyphoscoliosis, ocular manifestations, joint hypermobility, skin fragility and hyperextensibility, and other signs of connective-tissue involvement. The biochemical defect in most but not all patients is a deficiency in lysyl hydroxylase activity. Lysyl hydroxylase is an enzyme that catalyzes the formation of hydroxylysine in collagens and other proteins with collagen-like amino acid sequences. We have recently reported an apparently homozygous large-duplication rearrangement in the gene for lysyl hydroxylase, leading to the type VI variant of EDS in two siblings. We now report an identical, apparently homozygous large duplication in an unrelated 49-year-old female originally analyzed by Sussman et al. Our simple-sequence-repeat-polymorphism analysis does not support uniparental isodisomy inheritance for either of the two duplications. Furthermore, we indicate in this study that the duplication in the lysyl hydroxylase gene is caused by an Alu-Alu recombination in both families. Cloning of the junction fragment of the duplication has allowed synthesis of appropriate primers for rapid screening for this rearrangement in other families with the type VI variant of EDS.

Quentin, Y. 1994. A master sequence related to a free left Alu monomer (FLAM) at the origin of the B1 family in rodent genomes. Nucleic Acids Res. 22(12):2222-7.

The question of the origin of the B1 family of rodents is addressed. The modern B1 elements are similar to the left Alu monomer, but with a 9 bp deletion and a 29 bp duplication. Search of databases for B1 elements that do not exhibit those modern features revealed sequence fragments that are very similar to the free left Alu monomers (FLAMs) described in the primate genomes. In addition, the analysis reveals elements that have 10 bp or 7 bp deletion in place of the 9 bp deletion but without the 29 bp tandem duplication. The elements described define families of proto B1 elements (referred as PB1, PB1D10 and PB1D7) that appeared before the first modern B1 element. A phylogenetic reconstruction suggest that the origin of Alu and B1 families took place before the divergence between the primate and the rodent lineages and that each family has followed different evolutionary routes since this radiation.

Qureshi, S. J., D. J. Porteous, and A. J. Brookes. 1994. Alu-based vectorettes and splinkerettes. More efficient and comprehensive polymerase chain reaction amplification of human DNA from complex sources. Genet Anal Tech Appl. 11(4):95-101.

Alu-polymerase chain reaction (PCR) is widely used to amplify human specific fragments from complex heterologous DNAs, such as somatic cell hybrids or yeast artificial chromosome (YAC) recombinants, but the fragments amplified are limited in number and are nonrepresentative. This report describes a modified one-sided alu-PCR technique, which offers better representation of amplified sequences while maintaining human specificity. The method relies on the ligation of partially mismatched double-stranded oligonucleotides (vectorettes or splinkerettes) to endonuclease-restricted DNA and universal priming with a single alu-consensus primer, the complement to which is the unpaired region. Alu-vectorette and alu-splinkerette-PCR of two somatic cell hybrids results in a greater complexity of products than alu-PCR alone. The advantage of alu-splinkerette over alu-vectorette-PCR is the elimination of nonspecific priming owing to the presence of the vectorette primer and to an increase in the product size range, a consequence of the difference in the splinkerette design. Alu- splinkerette-PCR is a useful technique for generating new and more comprehensive markers of the human sequences contained in somatic cell hybrids and YACs.

Rubin, C. M., C. A. VandeVoort, R. L. Teplitz, and C. W. Schmid. 1994. Alu repeated DNAs are differentially methylated in primate germ cells. Nucleic Acids Res. 22(23):5121-7.

A significant fraction of Alu repeats in human sperm DNA, previously found to be unmethylated, is nearly completely methylated in DNA from many somatic tissues. A similar fraction of unmethylated Alus is observed here in sperm DNA from rhesus monkey. However, Alus are almost completely methylated at the restriction sites tested in monkey follicular oocyte DNA. The Alu methylation patterns in mature male and female monkey germ cells are consistent with Alu methylation in human germ cell tumors. Alu sequences are hypomethylated in seminoma DNAs and more methylated in a human ovarian dysgerminoma. These results contrast with methylation patterns reported for germ cell single-copy, CpG island, satellite, and L1 sequences. The function of Alu repeats is not known, but differential methylation of Alu repeats in the male and female germ lines suggests that they may serve as markers for genomic imprinting or in maintaining differences in male and female meiosis.

Schichman, S. A., M. A. Caligiuri, M. P. Strout, S. L. Carter, Y. Gu, E. Canaani, C. D. Bloomfield, and C. M. Croce. 1994. ALL-1 tandem duplication in acute myeloid leukemia with a normal karyotype involves homologous recombination between Alu elements. Cancer Res. 54(16):4277-80.

Rearrangements of the ALL-1 gene by reciprocal translocations involving chromosome band 11q23 are frequently associated with human acute leukemia. We have previously reported the detection of ALL-1 gene rearrangements in adult patients with acute myeloid leukemia lacking cytogenetic evidence of 11q23 translocations. These included 2 of 19 patients with normal karyotypes as well as 3 of 4 patients with trisomy 11 as a sole cytogenetic abnormality. Rearrangement of the ALL-1 genes in two of the patients with trisomy 11 was shown to result from a direct tandem duplication of a portion of the gene spanning exons 2-6. Here we report the characterization of the ALL-1 gene rearrangement in one of the previously reported acute myeloid leukemia patients with a normal karyotype. ALL-1 rearrangement in this patient results from a direct tandem duplication of a portion of the gene spanning exons 2-8. RNA polymerase chain reaction and DNA sequence analysis show that the partially duplicated ALL-1 gene is transcribed into mRNA capable of encoding a partially duplicated protein. Sequence analysis of the genomic fusion region provides evidence for Alu-mediated homologous recombination as a mechanism for partial duplication of the ALL-1 gene.

Seong, D. C., M. Y. Song, E. P. Henske, S. O. Zimmerman, R. E. Champlin, A. B. Deisseroth, and M. J. Siciliano. 1994. Analysis of interphase cells for the Philadelphia translocation using painting probe made by inter-Alu-polymerase chain reaction from a radiation hybrid. Blood. 83(8):2268-73.

Fluorescence in situ hybridization (FISH) probe for the identification of the Philadelphia (Ph) translocation [t(9;22) (q34;q11)] in chronic myelogenous leukemia cells was developed by inter-Alu-polymerase chain reaction of DNA from an interspecific somatic cell hybrid containing approximately 5 Mb of human DNA covering the ABL gene region on human chromosome 9q34. This probe was large enough to be effective in identifying the genomic domains yet small enough to resolve them in more than 90% of bone marrow interphase cells. Combination of the probe with a cosmid contig probe for the BCR region of chromosome 22 in two- color FISH reduced the frequency of false-positive identification of the Ph chromosome to less than 1%. The procedure allows detection of as few as 1% Ph+ cells independent of the cycling status or BCR/ABL expression level of cells, and the quantitation of non-Ph chromosome- containing interphase nuclei in the marrow of patients judged 100% Ph+ by standard cytogenetics.

Sharief, F. S., and S. S. Li. 1994. Nucleotide sequence of human prostatic acid phosphatase ACPP gene, including seven Alu repeats. Biochem Mol Biol Int. 33(3):561-5.

The protein-coding sequence of the human ACPP gene was shown to be interrupted by nine introns. The length of intron 1 was at least 5kb, while the sizes of introns 2 to 9 were estimated to be 3.4Kb, 0.5Kb, 5.5Kb, 5.0Kb, 2.0Kb, 5.0Kb, 2.5Kb and 3.5Kb, respectively. Therefore, the human ACPP gene has the size of more than 40kb. Thus far, the genomic sequence of 16,273 nucleotides, including the putative promoter region and seven Alu-repeats, have been determined. Three of these Alu- repeats are located immediately upstream to exon 1 and another is identified in intron 1. All of these Alu-sequences exhibit more than 85% identity to the consensus Alu-sequence.

Siden, T. S., J. Kumlien, T. Drumheller, S. E. Smith, D. Rohme, H. Lehrach, and D. I. Smith. 1994. Identification of human chromosome region 3p14.2-21.3-specific YAC clones using Alu-PCR products from a radiation hybrid. Somat Cell Mol Genet. 20(2):137-42.

Deletion of DNA sequences from at least three different regions on the short arm of human chromosome 3 (3p13-14, 3p21 and 3p25) are frequently observed during the development of many solid tumors, including lung cancers and renal cell carcinomas. In order to physically characterize the 3p21 region, we previously identified a radiation fusion hybrid that contained about 20 megabases of DNA from chromosome region 3p14.2- p21.3. In this study total Alu-PCR products from this hybrid were used as a probe to isolate 86 yeast artificial chromosomes (YAC) clones from a 620-kb average insert YAC library (ICRF). Sixty-nine Alu-PCR markers, generated from the YACs, and seven PCR primers were used to screen for overlaps between individual clones. Seven contigs were identified encompassing 32 YAC clones. Based on previous information about localization of the PCR primers, the three largest contigs could be assigned to smaller subregions between 3p14.2 and 3p21.3. By this work a large proportion of the 3p14.2-21.3 region is covered with large- insert YAC clones.

Soh, J., T. M. Mariano, G. Bradshaw, R. J. Donnelly, and S. Pestka. 1994. Generation of random internal deletion derivatives of YACs by homologous targeting to Alu sequences. DNA Cell Biol. 13(3):301-9.

To facilitate the manipulation of human genomic DNA in yeast artificial chromosome (YAC) clones, a plasmid to integrate the selective marker for antibiotic G418 resistance into YACs and to delete some of the human DNA fragments from YACs was constructed. The linearized integration/deletion plasmid, which contains Alu family sequences at both ends, can recombine with YACs containing human repetitive sequences via homologous recombination. The homologous recombination results in a random integration of the antibiotic G418-resistant gene into a human genomic Alu sequence, and in most cases, an internal deletion within the YAC. The YACs with internal deletions can be useful to identify the location of the genes if they produce functional knockouts. In those cases when the integration/deletion event disrupts the integrity of the gene so it no longer can produce a viable and functional mRNA in fused eukaryotic cells, the site of integration in the YAC thus serves as a marker for the inactivated gene. In this report we describe a model system to locate specific genes in YACs.

Spurdle, A. B., M. F. Hammer, and T. Jenkins. 1994. The Y Alu polymorphism in southern African populations and its relationship to other Y-specific polymorphisms [published erratum appears in Am J Hum Genet 1994 May;54(5):929]. Am J Hum Genet. 54(2):319-30.

Y-linked polymorphisms were studied in a number of African populations. The frequency of the alleles of a Y-specific Alu insertion polymorphism, termed the "Y Alu polymorphism," was determined in 889 individuals from 23 different African population groups. A trend in frequency was observed, with the insert largely absent in Caucasoid populations, at intermediate frequency in the Khoisan, and at high frequency in Negroids. The insert predates diversification of Homo sapiens, since it occurs in all groups. The Alu insertion is believed to result from a unique mutation event, and comparisons between this and several other Y-linked polymorphisms were carried out in an attempt to validate their usefulness in population and evolutionary studies. The p21A1/TaqI and pDP31/EcoRI polymorphisms and 49a/TaqI alleles were all shown to have arisen on more than one occasion, and evidence exists for a preraciation crossover event between the Y-linked pseudoautosomal XY275 locus and the Y chromosome pseudoautosomal boundary.

Tugendreich, S., Q. Feng, J. Kroll, D. D. Sears, J. D. Boeke, and P. Hieter. 1994. Alu sequences in RMSA-1 protein? [letter; comment]. Nature. 370(6485):106.

Vorce, R. L., B. Lee, and B. H. Howard. 1994. Methylation- and mutation-dependent stimulation of Alu transcription in vitro. Biochem Biophys Res Commun. 203(2):845-51.

Alu genes are GC-rich, highly repetitive genetic elements whose functions remain unknown. Members of this family are readily transcribed in vitro by RNA polymerase III, but RNA corresponding to only a small sub-set of Alu elements has been found in vivo. Based on the hypothesis that methylation of Alu elements affects their transcription, the transcriptional activity of unmethylated and methylated template DNA was assessed in vitro. It was found that methylation of a single CG site just 5' to Alu functions to stimulate transcription; the base composition in this region also affects transcriptional activity. These results indicate that the methylation state and sequence of DNA flanking Alu elements influence its transcription rate.

Wirkner, U., H. Voss, P. Lichter, W. Ansorge, and W. Pyerin. 1994. The human gene (CSNK2A1) coding for the casein kinase II subunit alpha is located on chromosome 20 and contains tandemly arranged Alu repeats. Genomics. 19(2):257-65.

We have isolated and characterized a 18.9-kb genomic clone representing a central portion of the human casein kinase II (CKII) subunit alpha gene (CSNK2A1). Using the whole clone as a probe, the gene was localized on chromosome 20p13. The clone contains eight exons whose sequences comprise bases 102 to 824 of the coding region of the human CKII alpha. The exon/intron splice junctions conform to the gt/ag rule. Three of the nine introns are located at positions corresponding to those in the CKII alpha gene of the nematode Caenorhabditis elegans. The introns contain eight complete and eight incomplete Alu repeats. Some of the Alu sequences are arranged in tandems of two or three, which seem to originate from insertions of younger Alu sequences into the poly(A) region of previously integrated Alu sequences, as indicated by flanking direct repeats.

Yoshiura, K. I., T. Kubota, H. Soejima, T. Tamura, Y. Izumikawa, N. Niikawa, and Y. Jinno. 1994. A comparison of GC content and the proportion of Alu/KpnI-repetitive sequences in a single dark- and light-band region from a human chromosome. Genomics. 20(2):243-8.

To obtain direct evidence for a molecular basis of differentiation between regular Giemsa dark (G)- and light (R)-band regions of human chromosomes, two regions of chromosome 11, q14-q22 (G-band) and q23-q25 (R-band), were microdissected. The DNA fragments were amplified by the linker-primer polymerase chain reaction and cloned into pUC19. Microclones from each library were then compared by colony hybridization with repetitive DNA sequences, by Southern blot hybridization of each microclone to total human genomic DNA and mouse- human hybrid cell DNA containing only human chromosome 11, and by sequencing of unique and Alu-repetitive clones. Among the G-band- derived microclones analyzed, 43.0% were single-copy (unique) sequences and 23.2% contained highly repetitive sequence elements; in the R-band- derived library, 54.2% were unique clones and 20.3% had highly repetitive elements. The G-band library was significantly richer in clones positive for KpnI sequences (4.1% in the G-band library vs 2.8% in the R-band library). No significant difference was found in the proportion of Alu repetitive clones present in the two libraries, but Class IV Alu sequence derivatives were more frequently observed in the R-library than in the G-library. Sequence analysis revealed no significant difference in GC content or in the ratio of CpG sequence to GpC dinucleotide between 30 microclones derived from G-bands and 29 microclones derived from R-bands.(ABSTRACT TRUNCATED AT 250 WORDS)

Zabarovsky, E. R., V. I. Kashuba, I. D. Kholodbnyuk, V. I. Zabarovska, E. J. Stanbridge, and G. Klein. 1994. Rapid mapping of NotI linking clones with differential hybridization and Alu-PCR. Genomics. 21(3):486-9.

For construction of a NotI restriction map of the human genome, the isolation and mapping of unique NotI linking clones represent important and critical steps. Recently we have shown that an Alu-PCR approach can be used for isolation of NotI linking clones from defined regions of the chromosomes. This represents a useful method for isolating and analyzing a small number of clones, but it would be laborious to use it for mapping many NotI linking clones simultaneously. Here we suggest another modification of Alu-PCR for rapid concurrent mapping of many NotI linking clones. The results clearly demonstrate the utility of this approach. Seventy-one random NotI linking clones were analyzed. Among them, 65 clones (91.5%) were correctly selected and mapped using this approach. With differential hybridization and Alu-PCR, a significant portion of all human NotI linking clones (> 30%) can be rapidly mapped to particular chromosomes or to defined regions of these chromosomes.

Zietkiewicz, E., C. Richer, W. Makalowski, J. Jurka, and D. Labuda. 1994. A young Alu subfamily amplified independently in human and African great apes lineages. Nucleic Acids Res. 22(25):5608-12.

A variety of Alu subfamilies amplified in primate genomes at different evolutionary time periods. Alu Sb2 belongs to a group of young subfamilies with a characteristic two-nucleotide deletion at positions 65/66. It consists of repeats having a 7-nucleotide duplication of a sequence segment involving positions 246 through 252. The presence of Sb2 inserts was examined in five genomic loci in 120 human DNA samples as well as in DNAs of higher primates. The lack of the insertional polymorphism seen at four human loci and the absence of orthologous inserts in apes indicated that the examined repeats retroposed early in the human lineage, but following the divergence of great apes. On the other hand, similar analysis of the fifth locus (butyrylcholinesterase gene) suggested contemporary retropositional activity of this subfamily. By a semi-quantitative PCR, using a primer pair specific for Sb2 repeats, we estimated their copy number at about 1500 per human haploid genome; the corresponding numbers in chimpanzee and gorilla were two orders of magnitude lower, while in orangutan and gibbon the presence of Sb2 Alu was hardly detectable. Sequence analysis of PCR- amplified Sb2 repeats from human and African great apes is consistent with the model in which the founding of Sb2 subfamily variants occurred independently in chimpanzee, gorilla and human lineages.

Almenoff, J. S., J. Jurka, and G. K. Schoolnik. 1994. Induction of heat-stable enterotoxin receptor activity by a human Alu repeat. J Biol Chem. 269(24):16610-7.

The heat-stable enterotoxins (ST) elaborated by enterotoxigenic Escherichia coli are a family of small cysteine-rich peptides that bind to specific epithelial receptors in the mammalian intestine, causing a secretory diarrhea. The expression of ST receptors is tightly regulated; they are found primarily in intestine, and their expression is developmentally modulated. One receptor for ST has been cloned, and its cDNA encodes a approximately 120-kDa particulate guanylyl cyclase (guanylyl cyclase-C). Recent studies suggest that there are additional ST receptors that are not homologous to guanylyl cyclase-C. We used an expression cloning strategy to identify intestinal mRNAs that lead to expression of ST receptor activity in transfected cells. Using an ST- specific affinity panning system, we identified a novel 1891-base pair cDNA that does not encode a receptor protein, but instead, consists primarily of untranslated sequence. This cDNA induced receptor activity in both COS and 293 embryonic kidney cells. Northern analysis of the T84 human intestinal cell line, from which this cDNA was cloned, suggests that it is part of a 7.8-kilobase mRNA transcript. This transcript was also identified in human small intestine and colon, as well as in several extra-intestinal tissues. Functional analysis of subcloned fragments reveals that ST binding activity is induced by a 457-base pair human Alu repetitive sequence within the cDNA and that the phenotype is independent of orientation. These findings suggest that a human Alu element induces expression of a unique ST receptor by a transacting mechanism. An unrelated Alu-rich genomic clone did not confer ST binding, suggesting that there may be structural and functional specificity within individual Alu sequences.

Bernard, L. E., and S. Wood. 1993. Human chromosome 5 sequence primer amplifies Alu polymorphisms on chromosomes 2 and 17. Genome. 36(2):302-9.

Members of the Alu family of repetitive elements occur frequently in the human genome and are often polymorphic. Techniques involving Alu element mediated polymerase chain reactions (Alu PCR) allow the isolation of region-specific human DNA fragments from mixed DNA sources. Such fragments are a source of region-specific Alu elements useful for the detection of Alu-related polymorphisms. A clone from human chromosome 5, corresponding to locus D5F40S1, was isolated using Alu PCR differential hybridization. Alu elements within this clone were investigated for the presence of potentially polymorphic 3' polyA tails. Primers were devised to amplify the 3' polyA tail of an Alu element present within the clone. One primer, D5F40S1-T, was specific to the DNA flanking the 3' end of the Alu element, and the other primer was homologous to sequences within the element. When these primers were used in PCR reactions, products from chromosomes 2 and 17 (loci D2F40S2 and D17F40S3) were amplified in addition to the expected product from chromosome 5. The most likely explanation for this nonspecific amplification is that the D5F40S1-T primer is located within a low-copy repetitive element that is 3' of the Alu element. This phenomenon presents a potential problem for the identification of region-specific Alu polymorphisms.

Braun, A., R. Bichlmaier, B. Muller, and H. Cleve. 1993. Molecular evaluation of an Alu repeat including a polymorphic variable poly(dA) (AluVpA) in the vitamin D binding protein (DBP) gene. Hum Genet. 90(5):526-32.

We investigated an Alu element at the end of intron 8 of the human vitamin D-binding protein (hDBP, group-specific component, GC) gene that shows a polymorphic poly(A) tail due to a variable number of tandem repeats (AluVpA) forming the 3' end of this member of the most abundant class of short interspersed repeated DNA element (SINES). The Alu element sequence in intron 8 of the GC gene was identical in all three common GC alleles (GC*1F, GC*1S, and GC*2) and could be classified as an Alu-Sa or Alu class-II sequence. The polymerase chain reaction was used to amplify selectively a fragment of about 200 bp containing the identified (TAAA)n repeat from genomic DNA of 188 unrelated human subjects. The size of the amplified products was determined by polyacrylamide gel electrophoresis. Four alleles (named GC-18*6, GC-I8*8, GCI8*10, and GC-18*11) were found that differed in size by multiples of four nucleotides. The allele frequencies ranged from 0.0053 to 0.8511 and the observed heterozygosity was 26%. The stable inheritance of this polymorphic patterned poly(A) sequence was confirmed by a segregation study of a highly informative family with 19 members. Statistically significant linkage disequilibrium between the AluVpA and the GC iso-electric focusing (IEF) phenotypes was found in a sample of 188 unrelated individuals and delta values were calculated from the observed haplotype distribution.

Brini, A. T., G. M. Lee, and J. P. Kinet. 1993. Involvement of Alu sequences in the cell-specific regulation of transcription of the gamma chain of Fc and T cell receptors. J Biol Chem. 268(2):1355-61.

The Fc epsilon RI-gamma chains are expressed in a variety of hematopoietic cells where they play a critical role in signal transduction. They are part of the high affinity IgE receptor in mast cells, basophils, Langerhans cells, and possibly other cells; a component of the low affinity receptor for IgG (Fc gamma RIIIA or CD16) in natural killer cells and macrophages; and part of the T cell antigen receptor in subsets of T cells. Here we have investigated the transcriptional regulation of the gamma chain gene by analyzing the 2.5- kilobase sequence upstream of the transcription start site. This sequence contains a promoter specific to cells of hematopoietic lineage. However, the tissue specificity of this promoter is only partial because it is active in all of the hematopoietic cells tested here, regardless of whether they constitutively express Fc epsilon RI- gamma chain transcripts. We have identified two adjacent cis-acting regulatory elements, both of which are part of an Alu repeat. The first (-445/-366) is a positive element active in both basophils and T cells. The second (-365/-264) binds to nuclear factors, which appear to be different in basophils and T cells, and acts as a negative element in basophils and as a positive one in T cells. Thus, this Alu repeat (90% identical to Alu consensus sequences) has evolved to become both a positive and negative regulator.

Bucala, R., A. T. Lee, L. Rourke, and A. Cerami. 1993. Transposition of an Alu-containing element induced by DNA-advanced glycosylation endproducts. Proc Natl Acad Sci U S A. 90(7):2666-70.

Advanced glycosylation endproducts react with DNA and cause mutations and DNA transposition in bacteria. To investigate the mutagenic effect of advanced glycosylation in mammalian cells, plasmid DNA containing the lacI mutagenesis marker was modified by advanced glycosylation endproducts in vitro, transfected into murine lymphoid cells, recovered, and analyzed for mutations, plasmid size changes, and the presence of shared insertion sequences. An 853-bp host-derived DNA sequence, designated INS-1, was identified as an insertion element common to plasmids recovered from multiple independent transfections. Modification of DNA by advanced glycosylation increased by 60-fold the apparent frequency of INS-1 transposition: from 0.025% to 1.5%. The INS- 1 element contains a 180-bp region that is homologous to the Alu repetitive sequence family. INS-1 was also observed to be present within larger insertional mutations and, in two cases, an apparently truncated version of INS-1 that lacks the Alu region was identified. These results demonstrate the experimental induction of DNA transposition involving mammalian chromosomal elements and suggest that advanced glycosylation may play a role in the formation of Alu- containing insertions that have been found to disrupt human genes.

Chang, D. Y., and R. J. Maraia. 1993. A cellular protein binds B1 and Alu small cytoplasmic RNAs in vitro. J Biol Chem. 268(9):6423-8.

B1 and Alu are sequence-homologous interspersed elements of unknown function that have expanded in the genomes of mice and humans, respectively. A minority of B1 and Alu sequences are expressed as small cytoplasmic RNAs. These RNAs have conserved a secondary structure motif also present in signal recognition particle (SRP) RNA despite substantial sequence divergence, whereas random B1 and Alu sequences have not. This RNA structure has also been conserved by the source sequences that gave rise to successive transpositions during B1 and Alu evolution. In the present work small cytoplasmic B1 and Alu RNAs synthesized in vitro were found to bind a cellular protein by mobility shift and UV cross-linking analyses. The mouse and human proteins demonstrate the same specificity to a panel of competitor RNAs. Results using mutated B1 RNA indicate that a single strand loop in the conserved Alu motif is essential for binding. Previous work by Strub et al. (Stub, K., Moss, J. B., and Walter, P. (1991) Mol. Cell. Biol. 11, 3949-3959) demonstrated that the Alu-specific protein SRP 9/14 does not footprint to this region of SRP RNA. This observation coupled with the failure of anti-SRP/9 antibodies to identify SRP 9/14 in the B1 RNA- protein complex as well as the apparent mass and other characteristics of the protein described here suggest that it is a novel B1-Alu RNA- binding protein. Conservation of primary and secondary structure by B1 and Alu small cytoplasmic RNAs as well as features of their specific expression and ability to interact with the conserved binding protein indicate that these RNAs are more homologous than previously appreciated.

Dutton, C. M., C. D. Bottema, and S. S. Sommer. 1993. Alu repeats in the human factor IX gene: the rate of polymorphism is not substantially elevated. Hum Mutat. 2(6):468-72.

Previous data suggested an elevated rate of polymorphism in Alu sequences. Direct genomic sequencing was performed on five Alu repeats in the factor IX gene in at least 20 unrelated males of European and Asian descent (40 kb total). In these Alu sequences, the estimated rate of polymorphism in Caucasians (HE = 7.1 x 10(-4); HN = 4.5 x 10(-4) is similar to previously examined nonrepetitive sequences in the factor IX gene, and about twofold lower than previous estimates of the average rate of polymorphism for the X-chromosome which utilized random genomic clones to detect RFLPs. The aggregate data on the rate of polymorphism in Alu sequences suggest that mutations due to gene conversions at these sites are infrequent.

Englander, E. W., A. P. Wolffe, and B. H. Howard. 1993. Nucleosome interactions with a human Alu element. Transcriptional repression and effects of template methylation. J Biol Chem. 268(26):19565-73.

Alu interspersed repetitive elements possess internal RNA polymerase III promoters which are strongly transcribed in vitro, yet these elements are nearly silent in somatic cells. To examine whether repression by chromatin proteins could contribute to the low level of Alu expression, a conserved Alu element from the fourth intron of the human alpha-fetoprotein gene was reconstituted with purified octamer or tetramer particles. Analysis of reconstitutes revealed that this Alu element directed translational and rotational positioning of octamers as well as tetramers. In vitro transcription experiments with reconstituted templates demonstrated that RNA polymerase III-dependent transcription of the Alu element was profoundly repressed by positioned octamer particles. Furthermore, complete CpG methylation of this template enhanced the capacity of tetramers to repress transcription.

Goldberg, Y. P., J. M. Rommens, S. E. Andrew, G. B. Hutchinson, B. Lin, J. Theilmann, R. Graham, M. L. Glaves, E. Starr, H. McDonald, and et al. 1993. Identification of an Alu retrotransposition event in close proximity to a strong candidate gene for Huntington's disease. Nature. 362(6418):370-3.

Huntington's disease (HD) is a late-onset autosomal dominant neuropsychiatric disorder presenting in mid-adult life with personality disturbance and involuntary movements, cognitive and affective disturbance, and inexorable progression to death. The underlying genetic defect has been mapped to chromosomal band 4p16.3 (refs 2, 3). Analysis of specific recombination events in some families with HD has further refined the location of the HD defect to a 2.2 megabase DNA interval. Using a direct complementary DNA selection strategy we have identified at least seven transcriptional units within the minimal region believed to contain the HD gene. Screening with one of the cDNA clones identified an Alu insertion in genomic DNA from two persons with HD which showed complete cosegregation with the disease in these families but was not found in 1,000 control chromosomes. Two genes including the previously identified alpha-adducin gene and another that encodes for a 12-kilobase transcript, map in close proximity to the Alu insertion site. The 12-kilobase transcript should be regarded as a strong candidate for the HD gene.

Hambor, J. E., J. Mennone, M. E. Coon, J. H. Hanke, and P. Kavathas. 1993. Identification and characterization of an Alu-containing, T-cell- specific enhancer located in the last intron of the human CD8 alpha gene. Mol Cell Biol. 13(11):7056-70.

Expression of the human CD8 alpha gene is restricted to cells of the lymphoid lineage and developmentally regulated during thymopoiesis. As an initial step towards understanding the molecular basis for tissue- specific expression of this gene, we surveyed the surrounding chromatin structure for potential cis-acting regulatory regions by DNase I hypersensitivity mapping and found four hypersensitive sites, three of which were T cell restricted. By using a reporter-based expression approach, a T-cell-specific enhancer was identified by its close association with a prominent T-cell-restricted hypersensitive sites in the last intron of the CD8 alpha gene. Deletion studies demonstrated that the minimal enhancer is adjacent to a negative regulatory element. DNA sequence analysis of the minimal enhancer revealed a striking cluster of consensus binding sites for Ets-1, TCF-1, CRE, GATA-3, LyF- 1, and bHLH proteins which were verified by electrophoretic mobility shift assays. In addition, the 5' end of the enhancer was composed of an Alu repeat which contained the GATA-3, bHLH, and LyF-1 binding sites. Site-directed mutation of the Ets-1 and GATA-3 sites dramatically reduced enhancer activity. The functional importance of the other binding sites only became apparent when combinations of mutations were analyzed. Taken together, these results suggest that the human CD8 alpha gene is regulated by the interaction of multiple T-cell nuclear proteins with a transcriptional enhancer located in the last intron of the gene. Comparison of the CD8 alpha enhancer with other recently identified T-cell-specific regulatory elements suggests that a common set of transcription factors regulates several T-cell genes.

Hellmann-Blumberg, U., M. F. Hintz, J. M. Gatewood, and C. W. Schmid. 1993. Developmental differences in methylation of human Alu repeats. Mol Cell Biol. 13(8):4523-30.

Alu repeats are especially rich in CpG dinucleotides, the principal target sites for DNA methylation in eukaryotes. The methylation state of Alus in different human tissues is investigated by simple, direct genomic blot analysis exploiting recent theoretical and practical advances concerning Alu sequence evolution. Whereas Alus are almost completely methylated in somatic tissues such as spleen, they are hypomethylated in the male germ line and tissues which depend on the differential expression of the paternal genome complement for development. In particular, we have identified a subset enriched in young Alus whose CpGs appear to be almost completely unmethylated in sperm DNA. The existence of this subset potentially explains the conservation of CpG dinucleotides in active Alu source genes. These profound, sequence-specific developmental changes in the methylation state of Alu repeats suggest a function for Alu sequences at the DNA level, such as a role in genomic imprinting.

Hutchinson, G. B., S. E. Andrew, H. McDonald, Y. P. Goldberg, R. Graham, J. M. Rommens, and M. R. Hayden. 1993. An Alu element retroposition in two families with Huntington disease defines a new active Alu subfamily. Nucleic Acids Res. 21(15):3379-83.

Alu repetitive elements represent the most common short interspersed elements (SINEs) found in primates, with an estimated 500,000 members in the haploid human genome. Considerable evidence has accumulated that these elements have dispersed in the genome by active transcription followed by retroposition, and that this process is ongoing. Sequence variation between the individual elements has lead to the hierarchical classification of Alu repeats into families and subfamilies. Young subfamilies that are still being actively transposed are of considerable interest, and the identification of one such subfamily (designated 'PV') has lead to the hypothesis that the most recent retroposition events are due to a single master Alu source gene. In the course of our search for the gene causing Huntington disease, we have detected an Alu retroposition event in two families. Sequence analysis demonstrates that this Alu element is not a member of the PV subfamily, but is similar to 5 other Alu elements in the GenBank database. Together, these Alu elements, all of which contain a 7 base-pair internal duplication, define a distinct subfamily, designated as the Sb2 subfamily, providing evidence for a second actively retroposing Alu source gene. These data provide support for multiple source genes for Alu retroposition in the human genome.

Iris, F. J., L. Bougueleret, S. Prieur, D. Caterina, G. Primas, V. Perrot, J. Jurka, P. Rodriguez-Tome, J. M. Claverie, J. Dausset, and et al. 1993. Dense Alu clustering and a potential new member of the NF kappa B family within a 90 kilobase HLA class III segment. Nat Genet. 3(2):137-45.

We have conducted a detailed structural analysis of 90 kilobases (kb) of the HLA Class III region from the Bat2 gene at the centromeric end to 23 kb beyond TNF. A single contig of 80 kb was sequenced entirely with a group of four smaller contigs covering 10 kb being only partly sequenced. This region contains four known genes and a novel telomeric potential coding region. The genes are bracketed by long, dense clusters of Alu repeats belonging to all the major families. At least six new families of MER repeats and one pseudogene are intercalated within and between the Alu clusters. The most telomeric 3.8 kb contains three potential exons, one of which bears strong homology to the ankyrin domain of the DNA binding factors NF kappa B and I kappa B.

Jurka, J. 1993. A new subfamily of recently retroposed human Alu repeats. Nucleic Acids Res. 21(9):2252.

Kigawa, K., K. Kihara, Y. Miyake, S. Tajima, T. Funahashi, T. Yamamura, and A. Yamamoto. 1993. Low-density lipoprotein receptor mutation that deletes exons 2 and 3 by Alu-Alu recombination. J Biochem (Tokyo). 113(3):372-6.

A deletion mutant in the low density lipoprotein receptor gene of a Japanese patient with heterozygous familial hypercholesterolemia was analyzed. Genomic Southern blotting showed abnormal size restriction fragments with BamHI (7.8 kb), EcoRI (3.8 kb), BglII (17 kb), KpnI (> 23 kb), EcoRV (13 kb), and XbaI (14 kb). The abnormal EcoRI fragment, 3.8 kb, was cloned into lambda phage vector, and the deleted region of 10 kb including exons 2 and 3 was identified. The nucleotide sequence around the deletion joint was determined. The sequence of the eight nucleotides in the deletion-joint region of the mutant gene was identical to the corresponding sequences of both introns 1 and 3 of the normal gene. The deletion seemed to occur by an unequal recombination between the Alu-like sequences in the same direction in introns 1 and 3.

Kochanek, S., D. Renz, and W. Doerfler. 1993. DNA methylation in the Alu sequences of diploid and haploid primary human cells. Embo J. 12(3):1141-51.

We have investigated DNA methylation in human Alu sequences, both in general and in specific Alu sequences associated with the genes for alpha 1 globin, tissue plasminogen activator (tPA), adrenocorticotropic hormone (ACTH) and angiogenin. We studied DNAs from lymphocytes, granulocytes, brain, heart muscle and sperm, and from the human HeLa and KB cell lines by using cleavage with methylation-sensitive restriction enzymes combined with Southern blot hybridization and by using genomic sequencing. The results can be summarized as follows. (i) In differentiated primary human cells, Alu elements are often highly methylated even when they are in very 5'-CG-3'-rich regions. This finding is not consistent with the notion that hypermethylation would be a sufficient condition in itself for 5'-CG-3' sequences to undergo loss of 5-methyl-deoxycytidine (5-mC) due to deamination and subsequent mutation. (ii) There are distinct differences in the levels of methylation in the specific Alu sequences. (iii) Alu elements in the DNA of haploid spermatozoa are much less methylated than in diploid cells. Preliminary data indicate that spermatozoa contain Alu-specific RNAs. (iv) The results of cell-free transcription experiments with Alu elements suggest that the in vitro transcription of Alu elements can be inhibited by 5'-CG-3' methylation. High levels of 5'-CG-3' methylation in Alu elements could contribute to their general transcriptional inactivity. (v) The patterns of methylation observed in the Alu elements and in the surrounding sequences are characterized by cell type specific interindividual concordance.

Lazaro, C., A. Gaona, A. Ravella, V. Volpini, T. Casals, J. J. Fuentes, and X. Estivill. 1993. Novel alleles, hemizygosity and deletions at an Alu-repeat within the neurofibromatosis type 1 (NF1) gene. Hum Mol Genet. 2(6):725-30.

Neurofibromatosis type 1 (NF1) (von Recklinghausen) is a common autosomal dominant disorder, characterised by the presence of peripheral neurofibromas, cafe-au-lait spots and Lisch nodules of the iris. Due to the high mutation rate at the NF1 locus, most patients are expected to have different mutations, limiting molecular analysis and genetic counseling to the identification of the mutation in each patient or family, or to the use of DNA polymorphisms. We have analysed an Alu-repeat polymorphic sequence (AAAT), located in intron 27 of the NF1 gene, in 70 NF1 and 40 CEPH families and we have detected several genetic and molecular abnormalities. In two families the NF1 individuals were hemizygous at the AAAT-repeat and/or at the CA-repeat of intron 27 of NF1, due to interstitial deletions, which include intron 27 to exon 37 of the NF1 gene. A 71-bp deletion at the Alu sequence was detected in non-NF1 chromosomes of members of three NF1 families. New alleles at the AAAT-repeat were found in one NF1 family and in three CEPH families giving a mutation rate for this AAAT-repeat of 0.36% per allele, which is one of the highest detected for a microsatellite locus.

Leeflang, E. P., W. M. Liu, I. N. Chesnokov, and C. W. Schmid. 1993. Phylogenetic isolation of a human Alu founder gene: drift to new subfamily identity [corrected] [published erratum appears in J Mol Evol 1994 Feb;38(2):204]. J Mol Evol. 37(6):559-65.

A severe bottleneck in the size of the PV Alu subfamily in the common ancestor of human and gorilla has been used to isolate an Alu source gene. The human PV Alu subfamily consists of about one thousand members which are absent in gorilla and chimpanzee DNA. Exhaustive library screening shows that there are as few as two PV Alus in the gorilla genome. One is gorilla-specific, i.e., absent in the orthologous loci in both human and chimpanzee, suggesting the independent retrotranspositional activity of the PV subfamily in the gorilla lineage. The second of these two gorilla PV Alus is present in both human and chimpanzee DNAs and is the single PV Alu known to precede the radiation of these three species. The orthologous Alu in gibbon DNA resembles the next older Alu subfamily. Thus, this Alu locus is originally templated by a non-PV source gene and acquired characteristic PV sequence variants by mutational drift in situ, consequently becoming the first member and presumptive founder of this PV subfamily.

Li, L., and P. F. Bray. 1993. Homologous recombination among three intragene Alu sequences causes an inversion-deletion resulting in the hereditary bleeding disorder Glanzmann thrombasthenia. Am J Hum Genet. 53(1):140-9.

The crucial role of the human platelet fibrinogen receptor in maintaining normal hemostasis is best exemplified by the autosomal recessive bleeding disorder Glanzmann thrombasthenia (GT). The platelet fibrinogen receptor is a heterodimer composed of glycoproteins IIb (GPIIb) and IIIa (GPIIIa). Platelets from patients with GT have a quantitative or qualitative abnormality in GPIIb and GPIIIa and can neither bind fibrinogen nor aggregate. Very few genetic defects have been identified that cause this disorder. We describe a kindred with GT in which the affected individuals have a unique inversion-deletion mutation in the gene for GPIIIa. Patient platelets lacked both GPIIIa protein and mRNA. Southern blots of patient genomic DNA probed with an internal 1.0-kb GPIIIa cDNA suggested a large rearrangement of this gene but were normal when probed with small GPIIIa cDNA fragments that were outside the mutation. Cytogenetics and pulsed-field gel analysis of the GPIIIa gene were normal, making a translocation or a very large rearrangement unlikely. Additional Southern analyses suggested that the abnormality was not a small insertion. We constructed a patient genomic DNA library and isolated fragments containing the 5' and 3' breakpoints of the mutation. The nucleotide sequence from these genomic clones was determined and revealed that, relative to the normal gene, the mutant allele contained a 1-kb deletion immediately preceding a 15-kb inversion. The DNA breaks occurred in two inverted and one forward Alu sequence within the gene for GPIIIa and in the left, right, and left arms, respectively, of these sequences. There was a 5-bp repeat at the 3' terminus of the inversion.(ABSTRACT TRUNCATED AT 250 WORDS)

Li, Y., A. Wong, P. Szabo, and D. N. Posnett. 1993. Human Tcrb-V6.10 is a pseudogene with Alu repetitive sequences in the promoter region. Immunogenetics. 37(5):347-55.

Tcrb-V6.10 represents an abnormal human V gene with an Alu insertion in the promoter, a point mutation of a conserved Cys at position 23, and a missing nonamer within the usually conserved recombinase signal sequence. Here it is shown that b-V6.10 is found in the genome of most individuals, is normally located in the Tcrb-V locus on chromosome 7, but is not rearranged or transcribed. Thus, it is likely that the abnormal signal sequence precludes recombination and that the Alu insertion results in a disabled promoter, indicating the functional importance of the affected regions. Tcrb-V6.10 probably evolved by duplication of an ancestral Tcrb V13-V6-V5 cassette, like other members of the large b-V6 subfamily, and more recently became inactivated into a pseudogene.

Liu, P., J. Siciliano, D. Seong, J. Craig, Y. Zhao, P. J. de Jong, and M. J. Siciliano. 1993. Dual Alu polymerase chain reaction primers and conditions for isolation of human chromosome painting probes from hybrid cells. Cancer Genet Cytogenet. 65(2):93-9.

A method for rapid and efficient production of chromosome- and chromosome-region specific probes for fluorescent in situ hybridization (FISH) detectable by simple fluorescent microscopy is described. The procedure is based on simultaneous use of two inter-Alu-polymerase chain reaction (PCR) primers for extraction of highly heterogeneous human DNA from interspecific somatic cell hybrids containing the chromosome regions of interest. Probes so produced do not hybridize to centromeric sequences and simultaneously band the target chromosomes, making them useful for unambiguous identification of chromosomal elements and breakpoints associated with cancer.

Liu, W. M., and C. W. Schmid. 1993. Proposed roles for DNA methylation in Alu transcriptional repression and mutational inactivation. Nucleic Acids Res. 21(6):1351-9.

Methylation at CpG dinucleotides to produce 5 methyl cytosine (5me-C) has been proposed to regulate the transcriptional expression of human Alu repeats. Similarly, methylation has been proposed to indirectly favor the transpositional activity of young Alu repeats by transcriptionally inactivating older Alu's through the very rapid transition of 5me-C to T. Both hypotheses are examined here by RNA polymerase III (Pol III) in vitro transcription of Alu templates using HeLa cell extracts. A limiting factor represses the template activity of methylated Alu repeats. Competition by methylated prokaryotic vector DNA's relieves repression, showing that the factor is not sequence specific. This competitor has no effect on the activity of unmethylated templates showing that the repressor is highly specific toward methylated DNA. While methylation of a single pair of CpG dinucleotides in the A box of the Poll III promoter is sufficient to cause repression, methylation elsewhere within the template also causes repression. The repressor causing these effects on the Pol III directed transcription of Alu repeats is thought to be a previously reported, repressor for Pol II directed templates. Young Alu repeats are transcriptionally more active templates than a representative older Alu subfamily member. Also, younger Alu's form stable transcriptional complexes faster, potentially giving them an additional advantage. The mutation of three CpG's to CpA's within and near the A box drastically decreases both the template activity and rate of stable complex formation by a young Alu member. The sensitivity of Alu template activity to CpG transitions within the A box partially explains the selective transpositional advantage enjoyed by young Alu members.

Mahadevan, M. S., M. A. Foitzik, L. C. Surh, and R. G. Korneluk. 1993. Characterization and polymerase chain reaction (PCR) detection of an Alu deletion polymorphism in total linkage disequilibrium with myotonic dystrophy. Genomics. 15(2):446-8.

The mutation causing myotonic dystrophy has been identified as an unstable trinucleotide CTG repeat located in the 3' untranslated region of a gene putatively encoding a serine-threonine protein kinase. The mutation has been reported to be in total linkage disequilibrium with an insertion/deletion polymorphism located within the kinase gene. To determine the nature of this polymorphism, we have sequenced this genomic fragment and have found that the sequence of this region consists of five consecutive Alu repeats. Further analysis suggests that the smaller of two alleles is actually due to a proposed deletion event that resulted in the loss of an equivalent of three Alu repeats. We have developed a PCR-based assay to detect this polymorphism, the closest, distal marker to the DM mutation.

Maraia, R. J., C. T. Driscoll, T. Bilyeu, K. Hsu, and G. J. Darlington. 1993. Multiple dispersed loci produce small cytoplasmic Alu RNA. Mol Cell Biol. 13(7):4233-41.

Alu repeats are short interspersed elements (SINEs) of dimeric structure whose transposition sometimes leads to heritable disorders in humans. Human cells contain a poly(A)- small cytoplasmic transcript of - 120 nucleotides (nt) homologous to the left Alu monomer. Although its monomeric size indicates that small cytoplasmic Alu (scAlu) RNA is not an intermediary of human Alu transpositions, a less abundant poly(A)- containing Alu transcript of dimeric size and specificity expected of a transposition intermediary is also detectable in HeLa cells (A. G. Matera, U. Hellmann, M. F. Hintz, and C. W. Schmid, Mol. Cell. Biol. 10:5424-5432, 1990). Although its function is unknown, the accumulation of Alu RNA and its ability to interact with a conserved protein suggest a role in cell biology (D.-Y. Chang and R. J. Maraia, J. Biol. Chem. 268:6423-28, 1993). The relationship between the -120- and -300-nt Alu transcripts had not been determined. However, a B1 SINE produces scB1 RNA by posttranscriptional processing, suggesting a similar pathway for scAlu. An Alu SINE which recently transposed into the neurofibromatosis 1 locus was expressed in microinjected frog oocytes. This neurofibromatosis 1 Alu produced a primary transcript followed by the appearance of the scAlu species. 3' processing of a synthetic -300-nt Alu RNA by HeLa nuclear extract in vitro also produced scAlu RNA. Primer extension of scAlu RNA indicates synthesis by RNA polymerase III. HeLa-derived scAlu cDNAs were cloned so as to preserve their 5'- terminal sequences and were found to correspond to polymerase III transcripts of the left monomeric components of three previously identified Alu SINE subfamilies.(ABSTRACT TRUNCATED AT 250 WORDS)

Marcus, S., D. Hellgren, B. Lambert, S. P. Fallstrom, and J. Wahlstrom. 1993. Duplication in the hypoxanthine phosphoribosyl-transferase gene caused by Alu-Alu recombination in a patient with Lesch Nyhan syndrome. Hum Genet. 90(5):477-82.

We have determined the structure, at the nucleotide sequence level, of a duplication in the hprt gene in a patient with Lesch-Nyhan syndrome (LN). The duplication extends over exons 7 and 8 and approximately 1.8 kb of the surrounding hprt sequence. The duplication junction is localized within two Alu sequences and has apparently been generated by unequal homologous recombination. This is the second reported case of a partial duplication of the hprt gene in an LN patient, and the first that involves an Alu-Alu recombination.

Martignetti, J. A., and J. Brosius. 1993. BC200 RNA: a neural RNA polymerase III product encoded by a monomeric Alu element. Proc Natl Acad Sci U S A. 90(24):11563-7.

We demonstrate that the BC200 RNA gene, which encodes a neural small cytoplasmic RNA, is a member of the most prodigious family of interspersed repetitive DNA and that its product represents an example of a primate tissue-specific RNA polymerase III transcript. The BC200 RNA gene is an early monomeric member and one of the few postulated transcriptionally active Alu sequences in this family of nearly half a million retropositionally amplified elements dispersed throughout the human genome. Furthermore, the isolation of two pseudogenes, BC200 beta and BC200 gamma, demonstrates the gene's transpositional ability. Interestingly, the BC200 beta pseudogene may have been generated by a conversion-like event after the human/chimpanzee divergence, resulting in an exchange of the left arm of a dimeric Alu element with the BC200 RNA coding sequence. Our data on conserved features of the active BC200 alpha gene suggest that its RNA product has been "exapted" into a function of the primate brain and provides a selective advantage to the species.

Mihovilovic, M., Y. Mai, M. Herbstreith, F. Rubboli, P. Tarroni, F. Clementi, and A. D. Roses. 1993. Splicing of an anti-sense Alu sequence generates a coding sequence variant for the alpha-3 subunit of a neuronal acetylcholine receptor. Biochem Biophys Res Commun. 197(1):137-44.

In this report we demonstrate that an alpha-3 acetylcholine receptor subunit transcriptional variant originates through alternative splicing of a complementary sequence of the right arm of an Alu element. This element is located within the 5.1 Kb intron found between exons 5 and 6 of the alpha-3 acetylcholine receptor subunit gene. The transcriptional variant originates from the normal splicing process and carries an in- frame stop codon. If translated, it should encode for a peptide lacking the 4th transmembrane domain of the normal subunit.

Moir, D. T., T. E. Dorman, F. Xue, N. S. Ma, V. P. Stanton, Jr., D. Housman, D. W. Bowden, W. W. Noll, and J. Mao. 1993. Rapid identification of overlapping YACs in the MEN2 region of human chromosome 10 by hybridization with Alu element-mediated PCR products. Gene. 136(1-2):177-83.

An overlapping set of 21 yeast artificial chromosomes (YACs) spanning the RET proto-oncogene [Takahashi et al., Oncogene 3 (1988) 571-578] and D10S102 markers on human chromosome 10 was isolated in a series of hybridization-based chromosomal walks in a YAC library. Genetic linkage analyses implicate this chromosomal region as the location of the gene (MEN2A) responsible for multiple endocrine neoplasia type 2A. Four YACs carrying a RET sequence-tagged site (STS) and two YACs carrying a D10S102 STS were used to initiate chromosome walks. These were based on hybridization of Alu element-mediated polymerase chain reaction (Alu- PCR) products from YACs to dot blots of Alu-PCR products from complex pools of YAC clones. The hybridization anchor content of YACs identified in the walks was confirmed by probing blots of Alu-PCR products from individual YACs and by comparing Alu-PCR fingerprints of each YAC. Ten hybridization-based Alu-PCR anchors and three STS anchors were ordered within eleven intervals created by the 21 overlapping YACs. The order of anchors requiring the fewest gaps in the YACs is consistent with the walking results and establishes the STS anchor order as D10S102-D10S94-RET. The overlapping set of YACs represents about 1.55 Mb of the human genome according to restriction mapping of four representative YACs in the contig. These results demonstrate the power of Alu-PCR hybridization for chromosomal walking and provide a rich source of overlapping YACs which can be used to identify candidate MEN2A genes.

Nguyen, T., A. Marchese, J. L. Kennedy, A. Petronis, S. J. Peroutka, P. H. Wu, and B. F. O'Dowd. 1993. An Alu sequence interrupts a human 5-hydroxytryptamine1D receptor pseudogene. Gene. 124(2):295-301.

Molecular cloning studies have now identified six HTR genes encoding the biosynthesis of the structurally homologous human serotonin (5- hydroxytryptamine; 5-HT) receptors, namely 5-HTR1A, 5-HTR1B, 5-HTR1C, 5- HTR1D, 5-HTR2 and 5-HTRS31. Several of these receptors are encoded by intronless genes, and we now report the cloning of another intronless serotonergic HTR gene. This gene was cloned by a method using the polymerase chain reaction. The nucleotide sequence of this gene is most closely homologous to the 5-HTR1D gene; however, several stop codons, frame shifts and deletions are present in the coding region suggesting that this is a pseudogene which could not encode a functional receptor. Sequence analysis also revealed that the coding sequence of this pseudogene is disrupted by insertion of a 283-bp Alu repeat sequence.

Panning, B., and J. R. Smiley. 1993. Activation of RNA polymerase III transcription of human Alu repetitive elements by adenovirus type 5: requirement for the E1b 58-kilodalton protein and the products of E4 open reading frames 3 and 6. Mol Cell Biol. 13(6):3231-44.

We found that transcription of endogenous human Alu elements by RNA polymerase III was strongly stimulated following infection of HeLa cells with adenovirus type 5, leading to the accumulation of high levels of Alu transcripts initiated from Alu polymerase III promoters. In contrast to previously reported cases of adenovirus-induced activation of polymerase III transcription, induction required the E1b 58-kDa protein and the products of E4 open reading frames 3 and 6 in addition to the 289-residue E1a protein. In addition, E1a function was not required at high multiplicities of infection, suggesting that E1a plays an indirect role in Alu activation. These results suggest previously unsuspected regulatory properties of the adenovirus E1b and E4 gene products and provide a novel approach to the study of the biology of the most abundant class of dispersed repetitive DNA in the human genome.

Porta, G., I. Zucchi, L. Hillier, P. Green, V. Nowotny, M. D'Urso, and D. Schlessinger. 1993. Alu and L1 sequence distributions in Xq24-q28 and their comparative utility in YAC contig assembly and verification. Genomics. 16(2):417-25.

The contents of Alu- and L1-containing TaqI restriction fragments were assessed by Southern blot analyses across YAC contigs already assembled by other means and localized within Xq24-q28. Fingerprinting patterns of YACs in contigs were concordant, and using software based on that of M. V. Olson et al. (1986, Proc. Natl. Acad. Sci. USA 83: 7826) to analyze digitized data on fragment sizes, fingerprinting itself could establish matches among about 40% of a test group of 435 YACs. At 100- kb resolution, both repetitive elements were found throughout the region, with no apparent enrichment of Alu or L1 in DNA of G compared to that found in R bands. However, consistent with a random overall distribution, delimited regions of up to 100 kb contained clusters of repetitive elements. The local concentrations may help to account for the reported differential hybridization of Alu and L1 probes to segments of metaphase chromosomes.

Riccio, M. L., and G. M. Rossolini. 1993. Unusual clustering of Alu repeats within the 5'-flanking region of the human lysozyme gene. DNA Seq. 4(2):129-34.

We report the nucleotide sequence of the 2.2-kb 5'-flanking region of the human lysozyme gene. Four Alu repeats are located within this upstream region. Classification and dating of these four Alu elements, as well as of the four Alu elements present within the human lysozyme structural gene, were performed. Transposition of the eight Alu repeats found in the human lysozyme locus has apparently occurred at four different times during the primate genome evolution. Considering that Alu repeats are interspersed throughout human DNA with an average spacing of 4 kb, the presence of eight such repeats within the 8-kb lysozyme gene region and, in particular, of four of them in the 2.2-kb region upstream of the structural gene, appears quite unusual.

Saegusa, Y., M. Sato, I. Galli, T. Nakagawa, N. Ono, S. M. Iguchi-Ariga, and H. Ariga. 1993. Stimulation of SV40 DNA replication and transcription by Alu family sequence. Biochim Biophys Acta. 1172(3):274-82.

The sequence motif GGAGGC (Alu core) is present in the Alu family repeats, where it is required for RNA polymerase III promoter function. This motif is also found in the SV40 origin (ori) of replication. Here, an oligonucleotide containing the Alu sequence was inserted into pSV2CAT, a plasmid composed of the SV40 enhancer/promoter/ori linked to the bacterial chloramphenicol acetyltransferase gene (CAT), to see the effect of the Alu sequence on SV40 DNA replication and transcription. Results of transfection experiments in human HeLa cells showed that the Alu sequence stimulated sequence-specifically replication and transcription in the SV40 system. Stimulation effects on DNA replication were observed when the Alu sequence was placed upstream of enhancer/promoter/ori in either orientation, while effects on transcription were detected only when it was inserted in the normal orientation. These effects correlate with sequence-specific binding of two proteins (40 kDa and 120 kDa) to this motif. In fact, binding was abolished by a mutation in the cognate sequence that disrupted stimulation of replication and transcription. Both proteins bind duplex DNA, while the 40 kDa one also binds the minus strand with high affinity.

Sims, H. F., M. L. Jennens, and M. E. Lowe. 1993. The human pancreatic lipase-encoding gene: structure and conservation of an Alu sequence in the lipase gene family. Gene. 131(2):281-5.

The isolation and characterization of the human gene (hPL) encoding pancreatic lipase is reported. The gene has 13 exons dispersed in about 20 kb of genomic DNA. A pseudogene of hPL was also partially characterized. An Alu sequence is conserved in the homologous introns of hPL and the lipoprotein lipase-encoding gene.

Takeishi, K., Y. Watanabe, K. Isono, and N. Horie. 1993. Cloning and structural analysis of a human thymidylate synthase pseudogene splitted by several Alu sequences. Nucleic Acids Symp Ser. 29:141-2.

An unidentified genomic DNA fragment of 2.4kb that is weakly hybridizable with thymidylate synthase (TS) cDNA was cloned from a human genomic DNA library. Sequencing of the cloned DNA fragment and comparison of the sequence with that of the known human TS cDNA revealed that the DNA fragment contained a human TS processed pseudogene with unusual features. Based on the rate of nucleotide substitutions for neutral mutations in the 3'-untranslated regions between the gene and the pseudogene, it was estimated that the human TS pseudogene was formed about 16 million years ago.

Thompson, J. F., M. E. Lira, D. B. Lloyd, L. S. Hayes, S. Williams, and L. Elsenboss. 1993. Cholesterol 7 alpha hydroxylase promoter separated from cyclophilin pseudogene by Alu sequence. Biochim Biophys Acta. 1168(2):239-42.

The promoter for human cholesterol 7-alpha hydroxylase has been cloned and sequenced. In the regions previously described, our sequence agrees well with one report but not with another. At position -469, we find a widespread MaeII polymorphism. At -2636, there is an Alu sequence flanked by runs of adenines. Upstream of the Alu sequence, there is a cyclophilin pseudogene oriented in the opposite direction.

Thorey, I. S., G. Cecena, W. Reynolds, and R. G. Oshima. 1993. Alu sequence involvement in transcriptional insulation of the keratin 18 gene in transgenic mice. Mol Cell Biol. 13(11):6742-51.

The human keratin 18 (K18) gene is expressed in a variety of adult simple epithelial tissues, including liver, intestine, lung, and kidney, but is not normally found in skin, muscle, heart, spleen, or most of the brain. Transgenic animals derived from the cloned K18 gene express the transgene in appropriate tissues at levels directly proportional to the copy number and independently of the sites of integration. We have investigated in transgenic mice the dependence of K18 gene expression on the distal 5' and 3' flanking sequences and upon the RNA polymerase III promoter of an Alu repetitive DNA transcription unit immediately upstream of the K18 promoter. Integration site- independent expression of tandemly duplicated K18 transgenes requires the presence of either an 825-bp fragment of the 5' flanking sequence or the 3.5-kb 3' flanking sequence. Mutation of the RNA polymerase III promoter of the Alu element within the 825-bp fragment abolishes copy number-dependent expression in kidney but does not abolish integration site-independent expression when assayed in the absence of the 3' flanking sequence of the K18 gene. The characteristics of integration site-independent expression and copy number-dependent expression are separable. In addition, the formation of the chromatin state of the K18 gene, which likely restricts the tissue-specific expression of this gene, is not dependent upon the distal flanking sequences of the 10-kb K18 gene but rather may depend on internal regulatory regions of the gene.

Tsongalis, G. J., W. B. Coleman, G. L. Esch, G. J. Smith, and D. G. Kaufman. 1993. Identification of human DNA in complex biological samples using the Alu polymerase chain reaction. J Forensic Sci. 38(4):961-7.

Alu-Polymerase chain reaction (PCR) was used to amplify human DNA from complex mixed sources of DNA. Amplification of human DNA sequences by Alu-PCR could be accomplished in samples containing low concentrations of template in the presence of excess heterologous DNA sequences. Thus, sensitivity and specificity are maintained in complex DNA mixtures allowing positive identification of the presence of human DNA sequences by this technique.

Vidal, F., E. Mougneau, N. Glaichenhaus, P. Vaigot, M. Darmon, and F. Cuzin. 1993. Coordinated posttranscriptional control of gene expression by modular elements including Alu-like repetitive sequences. Proc Natl Acad Sci U S A. 90(1):208-12.

We previously reported that in rat fibroblasts, accumulation of a set of mRNAs ("pIL genes") was modulated as a function of cell growth and transformation, at a posttranscriptional stage, and by a mechanism that depends on a short nucleotide sequence containing an ID repetitive element. In mouse fibroblasts, hybridization with rat pIL probes identified mRNAs with the same pattern of expression, which did not contain ID sequences but contained a different regulatory element, encompassing a repetitive sequence of the B1 family. Expression in mouse cells of a reporter beta-globin gene carrying this element inserted in its 3' noncoding region was growth- and transformation- dependent. The nucleotide sequences of two murine and of three rat pIL cDNAs showed clear similarities in the region immediately adjacent to the ID and B1 repeats. Both the repeat and the flanking sequence were required to confer on beta-globin constructs the pattern of expression characteristic of the pIL genes. The hypothesis is presented that repetitive sequences in the eukaryotic genome might be modular parts of complex regulatory elements ensuring the coordinated expression of various mRNA species.

Vidaud, D., M. Vidaud, B. R. Bahnak, V. Siguret, S. Gispert Sanchez, Y. Laurian, D. Meyer, M. Goossens, and J. M. Lavergne. 1993. Haemophilia B due to a de novo insertion of a human-specific Alu subfamily member within the coding region of the factor IX gene. Eur J Hum Genet. 1(1):30-6.

A de novo insertion of an Alu repeated DNA element was found within exon V of the factor IX gene in a patient with severe haemophilia B. The element interrupts the reading frame of the mature factor IX at glutamic acid 96 resulting in a stop codon within the inserted sequence. The Alu repeat is 322 bp long, and the 5' region is shortened by 38 bp. The insertion created a target site duplication of 15 bp consistent with retroposition, and contains a pure polyadenine tract of at least 78 resides at the 3' end. The nucleotide sequence agrees with a consensus for an Alu subfamily which is evolutionarily the most recently inserted, suggesting that it is an exact copy of a putative source gene. These observations indicate that retroposition of Alu elements is a continual process and a mechanism for generating human genetic defects.

Zhang, Z., S. Kolvraa, Y. Zhou, D. P. Kelly, N. Gregersen, and A. W. Strauss. 1993. Three RFLPs defining a haplotype associated with the common mutation in human medium-chain acyl-CoA dehydrogenase (MCAD) deficiency occur in Alu repeats. Am J Hum Genet. 52(6):1111-21.

Medium-chain acyl-CoA dehydrogenase (MCAD) deficiency is a common inborn error of fatty-acid oxidation and may cause sudden infant death. Previous studies revealed that (i) homozygosity for an A-to-G mutation at nucleotide 985 of the mRNA coding region (A985G) is an extremely common cause of MCAD deficiency and (ii) MCAD deficiency is strongly associated with a particular haplotype for RFLPs for BanII, PstI, and TaqI. TaqI allele 2 is always associated with the A985G mutation in human MCAD deficiency. In this study, we have delineated the molecular basis of the RFLPs for PstI, BamHI, and TaqI in the human MCAD gene. Our results prove that the three RFLPs are caused by point mutations in the 8 kb of DNA encompassing exons 8-10 of the human MCAD gene. The TaqI polymorphism is caused by a C-to-A substitution 392 bp upstream of the exon 8, and the PstI and BamHI polymorphisms are due to T-to-C and G-to-A substitutions, respectively, which are 727 and 931 bp downstream of exon 10 respectively. All three RFLPs lie within Alu repetitive sequences. Comparison of intronic sequences immediately following exon 10 from two normal individuals with different haplotypes showed that this region contains densely packed Alu repeats and is highly polymorphic. Our results are consistent both with a founder effect as the cause of the high prevalence of a single (A985G) mutation in MCAD deficiency and with its association with a particular haplotype for these intragenic RFLPs.

Bailey, A. D., and C. K. Shen. 1993. Sequential insertion of Alu family repeats into specific genomic sites of higher primates. Proc Natl Acad Sci U S A. 90(15):7205-9.

The presence of Alu family repeats is closely associated with interspecies length polymorphisms of certain genomic regions among different higher primates. By sequence analysis of cloned DNA, we show that one major cause for the length difference between the gibbon adult alpha-globin locus and those of human, orangutan, and Old World monkeys is the existence of multimeric Alu family repeats. Triplet Alu family repeats exist at two genomic sites of gibbon. Instead, singleton or doublet Alu family repeats are present at the orthologous positions in other higher primates. Sequence comparisons suggest that these doublet and triplet Alu repeats have been created by successive insertion of different singleton Alu repeat sequences, of approximately 300 bp, into the same genomic spot(s) during primate evolution. The approximate dates of insertion of these singleton Alu repeats support the concept of overlapping periods of active transposition or retroposition of Alu repeat subfamilies. This dynamic flow of Alu repeat sequences during primate evolution into the adult alpha-globin loci, but not beta-globin- like loci, is consistent with the previous finding that R-banding regions of the primate chromosomes are enriched in Alu repeats.

Benham, F., and P. Rowe. 1992. Use of Alu-PCR to characterize hybrids containing multiple fragments and to generate new Xp21.3-p22.2 markers. Genomics. 12(2):368-76.

Irradiation fragment hybrids potentially provide highly enriched sources of region-specific human DNA. However, such hybrids often contain multiple human pieces, not all of which can be easily detected. To develop specific resources for rapidly generating markers from Xp21.3-p22.2, we have single cell cloned two previously constructed irradiation hybrids that contain markers in this region and have achieved segregation of the different known fragments originally retained. Alu-PCR products were generated from subclones positive or negative for Xp21.3-p22.2 markers, and comparison of the ethidium bromide patterns between sister subclones facilitated identification of bands likely to map to particular regions; in contrast, subclones that shared markers but were derived from independent lines showed no overlap in ethidium bromide pattern. All Alu-PCR products from one subclone, 50K-19E, in which only three closely linked markers were detected (DXS41, DXS208, DXS274) were mapped back to their region of origin. Of 28 products, 15 mapped to Xp21.2-p22.2, and these make up a new set of regionally assigned markers. However, the mapping data identified four separate Xp fragments in 50K-19E, only one of which had been picked up by marker analysis. Mapping back gel-isolated Alu-PCR products from an irradiation hybrid prior to any cloning or screening generates a comprehensive profile of the human DNA retained and permits rapid selection of sequences derived only from the region of interest.

Chang, J. G., L. S. Lee, P. H. Chen, and Y. H. Chen. 1992. Hb Kaohsiung or New York: a T----A substitution at codon 113 of the beta-globin chain creates an Alu I cutting site. Hemoglobin. 16(1-2):123-5.

Chuat, J. C., A. Raisonnier, J. Etienne, and F. Galibert. 1992. The lipoprotein lipase-encoding human gene: sequence from intron-6 to intron-9 and presence in intron-7 of a 40-million-year-old Alu sequence. Gene. 110(2):257-61.

The complete nucleotide sequence of the 3877-bp segment spanning the 3' region of intron-6 to the 5' region of intron-9 of the human lipoprotein lipase (LPL)-encoding ten-exon gene, LPL, is reported. An Alu repeat present in intron-7 was found by sequence analysis to belong to the 40-55-million-year-old Alu-Se subclass.

Cole, C. G., K. Patel, J. Shipley, D. Sheer, M. Bobrow, D. R. Bentley, and I. Dunham. 1992. Identification of region-specific yeast artificial chromosomes using pools of Alu element-mediated polymerase chain reaction probes labeled via linear amplification. Genomics. 14(4):931-8.

The ability to identify large numbers of yeast artificial chromosomes (YACs) specific to any given genomic region rapidly and efficiently enhances both the construction of clone maps and the isolation of region-specific landmarks (e.g., polymorphic markers). We describe a method of preparing region-specific single-stranded hybridization probes from Alu element-mediated polymerase chain reaction (Alu-PCR) products of somatic cell hybrids for YAC library screening. Pools of up to 50 cloned Alu-PCR products from an irradiation-reduced hybrid containing 22q11.2-q13.1 were labeled to high specific activity by linear amplification using a single vector primer. The resulting single- stranded probes were extensively competed to remove repetitive sequences, while retaining the full complexity of the probe. Extensive coverage of the region by YACs using multiple probe pools was demonstrated as many YACs were detected more than once. In situ analysis using chosen YACs confirmed that the clones were specific for the region. Thus, this pooled probe approach constitutes a rapid method to identify large numbers of YACs relevant to a large chromosomal region.

Desmaze, C., J. Zucman, O. Delattre, G. Thomas, and A. Aurias. 1992. In situ hybridization of PCR amplified inter-Alu sequences from a hybrid cell line. Hum Genet. 88(5):541-4.

Polymerase chain reaction amplified products promoted by oligonucleotides complementary to the highly repetitive human Alu sequence can be used for in situ hybridization on metaphase chromosomes to investigate the human content of a hybrid cell line. The TC65 primer, which combines the advantages of promoting the amplification of large inter-Alu sequences together with only small flanking Alu sequences, enables a simple and precise characterization to be made, with a high signal to noise ratio. Total human DNA is an efficient competitor in the removal of non-specific signals. The use of this oligonucleotide should be considered in the characterization of the human content of hybrids or in the generation of specific reagents for chromosome decoration.

Edwards, M. C., and R. A. Gibbs. 1992. A human dimorphism resulting from loss of an Alu. Genomics. 14(3):590-7.

The molecular phylogeny of Alu and other repeated sequences in the human genome provides clues to events during primate evolution. A subclass of human Alu's has been previously identified as dimorphic insertions within members of the medium reiteration frequency (mer) class of repeats, reflecting the complicated sequence of insertion and radiation events leading to the current human genome structure. One dimorphic Alu is located within a previously unidentified mer family member, in the first intron of the human T4 (CD4) gene. The insertion (Alu+ allele) has a frequency of approximately 70% in Europeans and Africans and is homozygous in 20 Asian samples. Polymerase chain reaction amplification, direct DNA sequencing, and Southern analysis using oligonucleotide probes revealed that the Alu- allele was derived from the Alu+ allele by loss of part of the inserted sequence. Comparison with a tightly linked marker within the human genome and studies of baboon DNA samples revealed that the original insertion was a relatively early event in primate evolution, but that the Alu sequence loss leading to the dimorphism has occurred much more recently. Loss of Alu insertions therefore represents one mechanism for the generation of human Alu dimorphisms.

Elbein, S. C. 1992. Linkage disequilibrium among RFLPs at the insulin-receptor locus despite intervening Alu repeat sequences. Am J Hum Genet. 51(5):1103-10.

Multiple mutations of the insulin receptor (INSR) gene have been identified in individuals with extreme insulin resistance. These mutations have included recombination events between Alu repeat units in the tyrosine kinase-encoding beta-chain region of the gene. To evaluate the influence of Alu and dinucleotide repetitive sequences on recombination events within the insulin receptor gene, I examined the degree of linkage disequilibrium between RFLP pairs spanning the gene. I established 228 independent haplotypes for seven RFLPs (two each for PstI, RsaI, and SstI and one for MspI and 172 independent haplotypes which included an additional RFLP with BglII) from 19 pedigrees. These RFLPs span > 130 kb of this gene, and my colleagues and I previously demonstrated that multiple Alu sequences separate RFLP pairs. Observed haplotype frequencies deviated significantly from those predicted. Pairwise analysis of RFLP showed high levels of linkage disequilibrium among RFLP in the beta-chain region of the insulin receptor, but not between alpha-chain RFLPs and those of the beta-chain. Disequilibrium was present among beta-chain RFLPs, despite separation by one or more Alu repeat sequences. The very strong linkage disequilibrium which was present in sizable regions of the INSR gene despite the presence of both Alu and microsatellite repeats suggested that these regions do not have a major impact on recombinations at this locus.

Giordano, T., S. A. Johnson, K. Sakamoto, and B. H. Howard. 1992. Expression of Alu and 7SL RNA in Alzheimer's and control brains. Mech Ageing Dev. 64(1-2):13-20.

We investigated whether changes in expression of RNA polymerase III (pol III) or heterodisperse RNA polymerase II (pol II) transcripts hybridizing to Alu could be detected in Alzheimer's disease (AD). RNA samples obtained from AD and control brain tissues were examined by Northern analysis for Alu and 7SL RNA expression. All RNA samples contained a prominent band of approximately 300 nucleotides which corresponds to 7SL RNA, the Alu-homologous RNA component of the signal recognition particle. In addition, three small (i.e. less than 300 nucleotide) 7SL/Alu-hybridizing transcripts were detected. The two larger of the low molecular weight transcripts hybridized preferentially to the 7SL RNA probe, while the smallest transcript hybridized to the Alu probe. These transcripts and the heterodisperse RNA were variable in quantity and displayed a lack of correlation with AD.

Herring, W. J., M. McKean, N. Dracopoli, and D. J. Danner. 1992. Branched chain acyltransferase absence due to an Alu-based genomic deletion allele and an exon skipping allele in a compound heterozygote proband expressing maple syrup urine disease. Biochim Biophys Acta. 1138(3):236-42.

Branched chain alpha-ketoacid dehydrogenase assembles around a core of the acyltransferase components on the matrix side of the mitochondrial inner membrane. Autosomal recessive mutations in humans are known to decrease the function of this complex resulting in the clinical phenotype of maple syrup urine disease. Within this wide group of mutations are a subset which result in the antigenic absence of the acyltransferase protein of the complex. Here we describe two mutations in a compound heterozygote proband which result in this acyltransferase- negative phenotype. The mutant allele inherited from the father lacks 15-20 kilobases of genomic DNA resulting from a recombinational event between an intronic Alu sequence and coding sequence in the terminal exon. The mother's mutant allele contains a single base substitution in the -1 position of the 5' splice junction following exon 8. This G1002-- --A transition results in exon skipping producing two different mRNAs. The first lacks only exon 8 while the second lacks exons 8-10. All mRNAs for the acyltransferase found in cells from the proband have the potential to produce proteins ranging in size from 251-395 amino acids, the largest being 26 amino acids short of a full-length acyltransferase. The potential of these transcripts to produce protein is of interest since the patient is clinically responsive to pharmacologic treatment with thiamin, showing a higher tolerance to protein in the diet. The mechanism for this thiamin response remains to be explained.

Humphries, M. M., D. M. Sheils, S. A. Jordan, G. J. Farrar, R. Kumar-Singh, and P. Humphries. 1992. Alu polymorphism in the human type I Keratin (KRT14) gene. Hum Mol Genet. 1(6):453.

Iizuka, M., S. Mashiyama, M. Oshimura, T. Sekiya, and K. Hayashi. 1992. Cloning and polymerase chain reaction-single-strand conformation polymorphism analysis of anonymous Alu repeats on chromosome 11. Genomics. 12(1):139-46.

We have shown that many of the Alu repeats found in the GenBank database are polymorphic and that this polymorphism can be detected by a simple technique, single-strand conformation polymorphism (SSCP) analysis, after polymerase chain reaction (PCR) amplification of each repeat from DNA of individuals. Here, we describe a method for collecting many anonymous Alu repeats and their flanks in a chromosome- specific phage library and cloning them into plasmids. The flanking single-copy sequences of each repeat in the plasmid were then determined, and 20mer to 30mer segments of these sequences were used as primers for the PCR-SSCP analysis. Many new polymorphic DNA markers on chromosome 11 were obtained with this method. These markers can also serve as sequence-tagged sites for physical mapping of the genome.

Jang, K. L., M. K. Collins, and D. S. Latchman. 1992. The human immunodeficiency virus tat protein increases the transcription of human Alu repeated sequences by increasing the activity of the cellular transcription factor TFIIIC. J Acquir Immune Defic Syndr. 5(11):1142-7.

The HIV Tat protein is able to upregulate the transcription by RNA polymerase III of cotransfected or endogenous cellular Alu-repeated sequences in both HeLa and Jurkat T cells. This effect is mediated by an increase in the activity of transcription factor TFIIIC, which binds to the B box in the RNA polymerase III Alu promoter. This is the first example of an effect of the Tat protein on the transcription of a cellular gene or on the activity of a cellular transcription factor. The significance of this effect for the life cycle of HIV and its interaction with infected cells is discussed.

Jang, K. L., and D. S. Latchman. 1992. The herpes simplex virus immediate-early protein ICP27 stimulates the transcription of cellular Alu repeated sequences by increasing the activity of transcription factor TFIIIC. Biochem J. 284(Pt 3):667-73.

Infection with herpes simplex virus (HSV) results in an increase in the transcription of the endogenous Alu repeated sequence by RNA polymerase III. This effect is also observed in uninfected cells stably transformed with a plasmid expressing the HSV immediate-early protein ICP27 or in cells transfected with the gene encoding this protein. Both uninfected cells expressing ICP27 and cells infected with virus producing functional ICP27 display increased activity of the cellular transcription factor TFIIIC when compared with untreated cells. This increase is not observed, however, in cells infected with a mutant strain of virus which does not produce ICP27. Hence ICP27 induces elevated Alu transcription by activating transcription factor TFIIIC, which is the limiting factor for such transcription. This is the first report of increased activity of a cellular transcription factor during HSV infection, when most cellular gene activity is inhibited.

Lane, M. J., P. G. Waterbury, W. T. Carroll, A. M. Smardon, B. D. Faldasz, S. M. Peshick, S. Mante, C. S. Huckaby, R. E. Kouri, D. J. Hanlon, and et al. 1992. Variation in genomic Alu repeat density as a basis for rapid construction of low resolution physical maps of human chromosomes. Chromosoma. 101(5-6):349-57.

Human DNA restriction fragments containing high numbers of Alu repeat sequences can be preferentially detected in the presence of other human DNA restriction fragments in DNA from human: rodent somatic cell hybrids when the DNA is fragmented with enzymes that cleave mammalian DNA infrequently. This ability to lower the observed human DNA complexity allowed us to develop an approach to order rapidly somatic hybrid cell lines retaining overlapping human genomic domains. The ordering process also generates a relative physical map of the human fragments detected with Alu probe DNA. This process can generate physical mapping information for human genomic domains as large as an entire chromosome (100,000 kb). The strategy is demonstrated by ordering Alu-detected NotI fragments in a panel of mouse: human hybrid cells that span the entire long arm of human chromosome 17.

Leeflang, E. P., W. M. Liu, C. Hashimoto, P. V. Choudary, and C. W. Schmid. 1992. Phylogenetic evidence for multiple Alu source genes. J Mol Evol. 35(1):7-16.

A member of the young PV Alu subfamily is detected in chimpanzee DNA showing that the PV subfamily is not specific to human DNA. This particular Alu is absent from the orthologous loci in both human and gorilla DNAs, indicating that PV subfamily members transposed within the chimpanzee lineage following the divergence of chimpanzee from both gorilla and human. These findings and previous reports describing the transpositional activity of other Alu sequences within the human, gorilla, and chimpanzee lineages provide phylogenetic evidence for the existence of multiple Alu source genes. Sequences surrounding this particular Alu resemble known transcriptional control elements associated with RNA polymerase III, suggesting a mechanism by which cis- acting elements might be acquired upon retrotransposition.

Liu, W. M., E. P. Leeflang, and C. W. Schmid. 1992. Unusual sequences of two old, inactive human Alu repeats. Biochim Biophys Acta. 1132(3):306-8.

Two human Alu repeats terminating in an oligo(T) run rather than the usual A-rich 3' tail were isolated by library screening. Base sequence comparisons reveal that these unusual Alus are also exceptionally divergent from other Alu family members implying that they are evolutionarily old. Unlike other members of the family, they are not transcribed in vitro by RNA polymerase III (Pol III) suggesting a partial explanation for how Alu source genes might become inactive with age.

Ludwig, M., K. D. Wohn, W. D. Schleuning, and K. Olek. 1992. Allelic dimorphism in the human tissue-type plasminogen activator (TPA) gene as a result of an Alu insertion/deletion event. Hum Genet. 88(4):388-92.

Polymerase chain reaction and direct sequencing were used to investigate an amplified DNA fragment containing the suspected polymorphic site of all known intragenic restriction fragment length polymorphisms (RFLPs) within the human tissue-type plasminogen activator (TPA) gene. Sequence data obtained showed that these RFLPs were all generated by the presence or absence of one of the two Alu sequences located in intron h of the human TPA gene. Furthermore, one of the direct repeats flanking this Alu sequence was absent in the minor allele. In addition to indicating the presence of an Alu insertion in an ancestral human TPA gene, these findings suggest a slip- replication mechanism for the deletion of this Alu repeat, once inserted into the gene. As both alleles have been observed in similar frequencies among different ethnic groups, the insertion or subsequent deletion of this Alu sequence in the human TPA gene must have occurred early in human evolution.

Makela, T. P., E. Hellsten, J. Vesa, K. Alitalo, and L. Peltonen. 1992. An Alu variable polyA repeat polymorphism upstream of L-myc at 1p32. Hum Mol Genet. 1(3):217.

Maraia, R. J., D. Y. Chang, A. P. Wolffe, R. L. Vorce, and K. Hsu. 1992. The RNA polymerase III terminator used by a B1-Alu element can modulate 3' processing of the intermediate RNA product. Mol Cell Biol. 12(4):1500-6.

The dispersion of short interspersed elements (SINEs) probably occurred through an RNA intermediate. B1 is a murine homolog of the human SINE Alu; these elements are composed of 5' G + C-rich regions juxtaposed to A-rich tracts and are flanked by direct repeats. Internal promoters direct RNA polymerase III to transcribe B1 and Alu elements and proceed into the 3' flanking DNA until it reaches a (dT)4 termination signal. The resulting transcripts contain 3'-terminal oligo(U) tracts which can presumably base pair with the A-rich tract to form self-primed templates for reverse transcriptase and retrotransposition. Nuclear extracts from mouse tissue culture cells contain an RNA processing activity that removes the A-rich and 3'-terminal regions from purified B1 RNAs (R. Maraia, Nucleic Acids Res. 19:5695-5702, 1991). In this study, we examined transcription and RNA processing in these nuclear extracts. In contrast to results with use of purified RNA, nascent transcripts synthesized in nuclear extract by RNA polymerase III are not processed, suggesting that the transposition-intermediate-like RNA is shielded from processing by a protein(s). Alteration of an AATTTT TAA termination signal to a GCTTTTGC signal activated processing by greater than 100-fold in coupled transcription/processing reactions. A similar difference was found when expression was compared in frog oocytes. No difference in processing was found if the transcripts were made by T7 RNA polymerase in the presence of the nuclear extract, indicating that the different processing effects of the two terminators were dependent on synthesis by polymerase III. The modulation of processing of B1-Alu transcripts and the potential for retrotransposition of B1 and Alu DNA sequences are discussed.

McCombie, W. R., A. Martin-Gallardo, J. D. Gocayne, M. FitzGerald, M. Dubnick, J. M. Kelley, L. Castilla, L. I. Liu, S. Wallace, S. Trapp, and et al. 1992. Expressed genes, Alu repeats and polymorphisms in cosmids sequenced from chromosome 4p16.3. Nat Genet. 1(5):348-53.

The sequences of three cosmids (90 kilobases) from the Huntington's disease region in chromosome 4p16.3 have been determined. A 30,837 base overlap of DNA sequenced from two individuals was found to contain 72 DNA sequence polymorphisms, an average of 2.3 polymorphisms per kilobase (kb). The assembled 58 kb contig contains 62 Alu repeats, and eleven predicted exons representing at least three expressed genes that encode previously unidentified proteins. Each of these genes is associated with a CpG island. The structure of one of the new genes, hda1-1, has been determined by characterizing cDNAs from a placental library. This gene is expressed in a variety of tissues and may encode a novel housekeeping gene.

Meese, E. U., P. S. Meltzer, P. W. Ferguson, and J. M. Trent. 1992. Alu-PCR: characterization of a chromosome 6-specific hybrid mapping panel and cloning of chromosome-specific markers. Genomics. 12(3):549-54.

The Alu-polymerase chain reaction (Alu-PCR) was applied to selectively amplify DNA sequences from human chromosome 6 using a single primer (A1) directed to the human Alu consensus sequence. A specific amplification pattern was demonstrated for a panel of eight somatic cell hybrids containing different portions of chromosome 6. This PCR pattern permits the identification of submicroscopic DNA alterations and can be utilized as a reference for additional chromosome 6-specific hybrids. To obtain new chromosome 6-specific markers we established two libraries from PCR-amplified sequences using two somatic cell hybrids (MCH381.2D and 640-5A). Out of a total of 109 clones that were found to be chromosome 6 specific, 13 clones were regionally assigned. We also included a procedure that allows the isolation of chromosome 6-specific markers from hybrids that contain human chromosomes other than 6. Our results will contribute to the molecular characterization of chromosome 6 by fostering characterization of somatic cell hybrids and by the generation of new regionally assigned DNA markers.

O'Brien, C. A., and J. B. Harley. 1992. Association of hY4 pseudogenes with Alu repeats and abundance of hY RNA- like sequences in the human genome. Gene. 116(2):285-9.

Three loci having homology with the small human cytoplasmic RNA, hY4, were isolated from human genomic DNA libraries and sequenced. Each sequence contains dispersed mismatches as compared with hY4 RNA, is followed by an A-rich or A + T-rich sequence, and is bordered by direct repeats. Each of these loci, therefore, appears to constitute a small RNA class-III pseudogene. Surprisingly, two of the three loci are associated with Alu repeats. In the hY4.B7 locus, the hY4 sequence has integrated into the tail of an Alu element and in the hY4.F2 locus, an Alu sequence has inserted into the hY4 tail, confirming that A-rich tracts are preferential targets for retroposition. In addition, Southern blots with probes for each of the four hY RNAs indicate that hY RNA-like sequences are abundant in the human genome.

Onno, M., T. Nakamura, J. Hillova, and M. Hill. 1992. Rearrangement of the human tre oncogene by homologous recombination between Alu repeats of nucleotide sequences from two different chromosomes. Oncogene. 7(12):2519-23.

The rearranged region of the tre oncogene originating from chromosomes 5q23q31 and 18q12 was cloned from tumor genomic DNA, sequenced and aligned with wild-type sequences cloned from a normal human genomic library. In the breakpoint region each wild-type sequence contained two Alu repeats. The recombination occurred between the 3'-most Alu from chromosome 5 and the 5'-most Alu from chromosome 18 and, consequently, resulted in a hybrid Alu flanked with one Alu on either side. The recombinant joint was located to a 20-bp homology region in left arms of the Alu repeats involved in recombination. The same homology region was identified in the hybrid Alu of the rearranged tre. At its 5' extremity the homology region overlaps the B box of Alu-borne RNA polymerase III promoter. The 100% identity score in the region of homology suggests that the recombination process was conservative and not error prone.

Peltoketo, H., V. Isomaa, and R. Vihko. 1992. Genomic organization and DNA sequences of human 17 beta-hydroxysteroid dehydrogenase genes and flanking regions. Localization of multiple Alu sequences and putative cis-acting elements. Eur J Biochem. 209(1):459-66.

Genomic 17 beta-hydroxysteroid-dehydrogenase (17-HSD) clones were isolated from a human leucocyte genomic library using cDNA encoding human placental 17-HSD as a probe. The overlapping fragments spanned more than 21 kbp containing the duplications, 6.2 kbp of each, as well as 7 kbp upstream and 1.6 kbp downstream from the duplicated sequences. 17 complete and eight partial Alu elements were clustered in this area, covering about 30% of the region, including the borders of the duplications. Each duplication contained a 17-HSD gene and a conserved region of 1.56 kbp with 98% intercopy similarity. The exon structure of the 17-HSD gene II corresponded to the known cDNA species, but both genes contained a possible promoter region with TATA, GC and inverse CAAT boxes. The 5' flanking regions contained sequences similar to the consensus sequences of cis-acting elements, defined as regulators of 17- HSD gene expression. These putative sequences included estrogen and progesterone/glucocorticoid-response elements and a cyclic-AMP regulatory element.

Perna, N. T., M. A. Batzer, P. L. Deininger, and M. Stoneking. 1992. Alu insertion polymorphism: a new type of marker for human population studies. Hum Biol. 64(5):641-8.

A PCR-based method was used to screen 462 individuals from Japan, Papua New Guinea, Indonesia, and Australia for an Alu family insertion polymorphism. The frequency of this Alu insertion shows significant heterogeneity among island subgroups of the Indonesian sample and between the Japanese-Indonesian populations and the Australian-New Guinean populations. The simple, rapid PCR-based screening technique and the significant frequency differences among populations demonstrate that Alu insertion polymorphisms are potentially valuable markers for studies of the evolutionary history and migration patterns of modern humans.

Quentin, Y. 1992. Fusion of a free left Alu monomer and a free right Alu monomer at the origin of the Alu family in the primate genomes. Nucleic Acids Res. 20(3):487-93.

In the primate genome, a typical Alu element corresponds to a dimeric structure composed of two different but related monomeric sequences arranged in tandem. However, the analysis of primate sequences found in GenBank reveals the presence of free left and free right Alu elements. Here, we report the statistical study of those monomeric elements. We found that only a small fraction of them results from a deletion of a dimeric Alu sequence. The majority derives from the amplification of monomeric progenitor sequences and constitutes two families of monomeric elements: a family of free left Alu monomers that is composed of two subfamilies and a small family of free right Alu monomers. Both families predated the dimeric Alu elements, and a phylogenetic analysis strongly suggests that the first progenitor of the dimeric Alu family arose through the fusion of a free left monomer with a free right monomer.

Quentin, Y. 1992. Origin of the Alu family: a family of Alu-like monomers gave birth to the left and the right arms of the Alu elements. Nucleic Acids Res. 20(13):3397-401.

The Alu dimeric elements are a common feature of the primate genomes, where they constitute a family of related sequences (1). The identification of a free left Alu monomer (FLAM) family plus a free right Alu monomer (FRAM) family suggests that the dimeric structure results from the fusion of a FLAM sequence with a FRAM sequence (2). Here, we describe a very old Alu-like monomeric family, referred to as FAM for fossil Alu monomer. This family arose from a 7SL RNA sequence and gave birth to the FLAM and FRAM families. From the results obtained, the evolution of the Alu family can be subdivided into two phases. The first phase, which involves only monomeric elements, is characterized by deep remodelling of the progenitor sequences and ends with the appearance of the first Alu dimeric element through the fusion of a FLAM and a FRAM element. The second phase, still in progress, starts with the first Alu dimeric element. This phase is characterized by the stabilization of the progenitor sequences.

Sainz, J., L. Pevny, Y. Wu, C. R. Cantor, and C. L. Smith. 1992. Distribution of interspersed repeats (Alu and Kpn) on NotI restriction fragments of human chromosome 21. Proc Natl Acad Sci U S A. 89(3):1080-4.

Interspersed repeated sequences (Alu and Kpn) were used as probes to detect a set of Not I restriction fragments of human chromosome 21 from the hybrid cell line WAV17. Forty different Not I fragments, ranging in size from less than 0.05 megabase (Mb) to 7.0 Mb, were identified. The total length of these fragments was 47.3 Mb. This length provides an estimate of the minimum size of the chromosome and a minimum number of fragments to be ordered to create a complete restriction map. The average length Not I fragment is 1.2 Mb. Alu and Kpn fragments are not always coincident: a 2.9-Mb fragment is detected with Kpn but not with Alu, and 13 fragments, ranging from less than 0.05 Mb to 5.6 Mb, are detected with Alu but not with Kpn; the 26 remaining fragments, covering 75% (35.3 Mb) of the total length, are detected with both repetitive probes. The presence of so many noncoincident fragments and the high variation of the hybridization signal intensities of the fragments suggest a very nonuniform distribution of Kpn and Alu repeats.

Sen, S., S. Rani, E. J. Freireich, R. Hewitt, and S. A. Stass. 1992. Detection of extrachromosomal circular DNA sequences from tumor cells by an alkaline lysis, Alu-polymerase chain reaction technique. Mol Carcinog. 5(2):107-10.

Extrachromosomal circular DNAs ranging in size from submicroscopic molecules of approximately 100 kb to cytogenetically resolvable structures of 1000+ kb called minute and double-minute chromosomes have been shown to harbor amplified genes in primary tumor cells, tumor cell lines, and drug-resistant cells grown in vitro. The presence of these molecules in transformed and malignant cells trends to reflect genetic instability and also suggests that role in tumor progression. Using a colon carcinoma cell line, we developed a technique to detect extrachromosomal circular DNA-specific sequences by Alu-polymerase chain reaction. Circular DNA was enriched by selective alkaline denaturation of genomic DNA. We have successfully performed this procedure with a minimum of 5 x 10(5) cells. The technique does not require any prior knowledge of the sequences located on the covalent circular DNA molecules for their detection. The procedure should be useful as a routine screen of primary tumor cells for the presence of extrachromosomal circular DNA and should permit the preparation of specific probes ot aid in their detailed characterizations.

Shriver, M. D., G. Siest, and E. Boerwinkle. 1992. Length and sequence variation in the apolipoprotein B intron 20 Alu repeat. Genomics. 14(2):449-54.

We have developed a single-stranded conformation polymorphism (SSCP) protocol for typing both sequence and length variations in an Alu element located in intron 20 of the human apolipoprotein B (apo B) gene. Using the polymerase chain reaction (PCR), we simultaneously amplified and isotopically labeled the apo B intron 20 Alu. The Alu tail, which is composed of two arrays of variable numbers of tandem repeats, (TTTX)y (X = A or G) and (T)z, was separated from the rest of the PCR product by restriction enzyme digestion with PstI. Length variation in the Alu tail (IN20-REP) was thus separated from sequence variation in the Alu body (IN20-SEQ), rendering the SSCP patterns both eaiser to interpret and more informative. In a sample of 242 unrelated individuals from Nancy, France, we observed 11 SSCP alleles at the IN20- SEQ locus that differed only in sequence. At the IN20-REP locus, we observed 7 alleles that differed in both sequence and length. All alleles at both loci were subcloned and sequenced. One additional allele that did not undergo a detectable mobility shift in SSCP gels was uncovered at each locus during sequencing of the SSCP alleles. The additional IN20-SEQ allele was typed by restriction enzyme digestion. Although the number of IN20-SEQ and IN20-REP alleles was large, most were uncommon; the three most common alleles at each locus represented more than 94% of those sampled. We also typed the children of the 242 unrelated French individuals, enabling verification of the Mendelian segregation of the two loci and construction of haplotypes.(ABSTRACT TRUNCATED AT 250 WORDS)

Sinnett, D., C. Richer, J. M. Deragon, and D. Labuda. 1992. Alu RNA transcripts in human embryonal carcinoma cells. Model of post- transcriptional selection of master sequences. J Mol Biol. 226(3):689-706.

Alu master sequences colonized the human genome using RNA as amplification intermediate. To understand this phenomenon better we isolated and analyzed Alu RNA from NTera2D1 pluripotential cells. Northern hybridization, primer extension, cDNA cloning and sequencing data are congruent and demonstrate a low level of Alu specific transcription. These bona fide RNA Polymerase III Alu transcripts, although enriched in the cytoplasm, are not dominated by a single master species but rather originate from a variety of loci. However, when compared with the genomic average, or to repeats from RNA Polymerase II co-transcripts, they belong to the youngest group of Alu subfamilies (p less than 0.001) and have a higher content of intact CpG- dinucleotides. This suggests that Alu transcription is influenced both by mutations and the genomic context, and points to a possible role of DNA methylation in silencing the bulk of genomic repeats. Because of the heterogeneity of Alu transcripts a post-transcriptional selection mechanism recruiting Alu master sequences for retroposition is required. We propose that Alu RNA masters could have evolved as selfish satellites to a more complex retroposition system equipped with a reverse transcriptase activity and that their structure was conserved through "phenotypic" selection of the RNA level.

Targovnik, H., C. Paz, D. Corach, and D. Christophe. 1992. The 5' region of the human thyroglobulin gene contains members of the Alu family. Thyroid. 2(4):321-4.

Repeated sequences were identified in the 5' region of the human Tg gene in introns 4, 5, 10, and 11. Another repeated cluster was located in the 5' flanking sequences, approximately 6 Kb upstream from the first exon. The nucleotide sequence analysis indicated that these repeated sequences are members of the Alu family. The homology between the sequences of the intron 4 and the Alu consensus was 86%. The Alu member studied was oriented in the direction of transcription of the Tg.

Tomilin, N. V., V. M. Bozhkov, E. M. Bradbury, and C. W. Schmid. 1992. Differential binding of human nuclear proteins to Alu subfamilies. Nucleic Acids Res. 20(12):2941-5.

Several diagnostic differences that distinguish human Alu subfamilies are clustered just downstream from the B box of the RNA polymerase III promoter; we tentatively refer to this diagnostic region as the DB box. Assuming that this region might determine the relative transcriptional activity of Alu subfamilies, we examined the interaction of nuclear proteins with DB box sequences representing different Alu subfamilies. Gel mobility shift assays suggest the existence of two factors which discriminate among the DB boxes of different Alu subfamilies: 1) An abundant, ca. 50 kd, protein binds more stably to a young 'PV' Alu subfamily (PVS) than to the older major subfamily (MS). 2) Methylation of CpG dinucleotides stimulates the binding of a less abundant, ca. 70 kd, protein to the DB boxes of younger Alu subfamilies.

Zietkiewicz, E., M. Labuda, D. Sinnett, F. H. Glorieux, and D. Labuda. 1992. Linkage mapping by simultaneous screening of multiple polymorphic loci using Alu oligonucleotide-directed PCR. Proc Natl Acad Sci U S A. 89(18):8448-51.

We present the use of our recently described multiple-loci polymorphic DNA markers ("alumorphs") for linkage mapping of the human genome. By using the polymerase chain reaction (PCR) with an Alu-specific primer we could reveal, in a single experiment, up to 20 genomic polymorphisms seen as the presence or absence of amplified DNA fragments originating from genomic segments flanked by Alu repeats. Using this approach we examined genomic DNA samples from two families with a history of pseudovitamin D-deficiency rickets (PDDR), an autosomal recessive disorder. An indication of linkage with the PDDR phenotype was found for one of the polymorphic bands, denoted 30A. A significant linkage [logarithm-of-odds (lod) score greater than 3.0] was obtained between this polymorphism and a number of chromosome 12q markers tightly linked to PDDR. The 30A band specifically hybridized to DNA digests from hybrid cell lines carrying a human chromosome 12, thus independently assigning the 30A marker to this chromosome. Since Alu elements are ubiquitous in human DNA, the use of alternative Alu-specific primers, which reveal different sets of Alu-flanked loci, should provide an efficient and rapid approach to human genetic mapping.

Arveiler, B., and D. J. Porteous. 1992. Distribution of Alu and L1 repeats in human YAC recombinants. Mamm Genome. 3(12):661-8.

Evidence is accumulating that the two major families of interspersed repeated human DNA sequences, Alu and L1, are not randomly distributed. However, only limited information is available on their relative long- range distribution. We have analyzed a set of randomly selected, human Chromosome (Chr) 11-specific YAC recombinants constituting a total length of about 2 Mbp for the local and global distribution of Alu and L1 repeats: the data show a strong asymmetry in the distribution of these two repeat classes and give weight, at the long-range molecular level, to previous studies indicating their partition in the human genome; they also suggest a strong tendency for L1 repeats to cluster, with a higher proportion of full-length elements than expected.

Batzer, M. A., V. A. Gudi, J. C. Mena, D. W. Foltz, R. J. Herrera, and P. L. Deininger. 1991. Amplification dynamics of human-specific (HS) Alu family members. Nucleic Acids Res. 19(13):3619-23.

We have investigated the distribution of several recently inserted Alu family members within representatives of diverse human groups. Human population studies using 65 unrelated human DNA samples, as well as a familial study to test inheritance, showed that individual Alu family members could be divided into three groups. The first group consisted of relatively older Alu family members which were monomorphic (homozygous) throughout the population tested (HS C3N1 and C4N6). The second group (HS C4N2, C4N5 and C4N8), apparently inserted into other repetitive regions of the genome, resulting in inconclusive results in the PCR test used. However, it is clear that these particular Alu insertions were present in a majority if not all of the loci tested. The third group was comprised of three dimorphic Alu family members (HS C2N4, C4N4 and TPA 25). Only a single Alu family member (TPA 25) displayed a high degree of dimorphism within the human population. This latter example also showed different allele frequencies in different human groups. The isolation and characterization of additional highly dimorphic Alu family members should provide a useful tool for human population genetics.

Carter, P. E., C. Duponchel, M. Tosi, and J. E. Fothergill. 1991. Complete nucleotide sequence of the gene for human C1 inhibitor with an unusually high density of Alu elements. Eur J Biochem. 197(2):301-8.

The complete (17159 bp) nucleotide sequence of the gene for the human C1 inhibitor has been determined. The transcription initiation site was examined by primer extension using human liver mRNA, and the messenger 5'-end sequence was determined on clones obtained by the anchored polymerase chain reaction. The gene of this serpin molecule is split by seven introns, with junctions of phases zero and one. An outstanding feature of the intron sequences is the occurrence of 17 AluI repeats of all four ancestral subgroups, indicating that the gene has been invaded during consecutive waves of Alu amplification, including a recent one. These Alu repeats form the sites of deletion and insertion in several known lesions in the C1-inhibitor gene. There is no obvious promoter site of the TATA-box type at the 5' end of the gene, but instead it contains a region of potential H-DNA structure similar to that found upstream of the human c-myc gene.

Chang, C. Y., and B. C. Chung. 1991. Characterization of Alu repeats surrounding the human ferredoxin- encoding gene. Gene. 104(2):283-4.

Three Alu sequences have been identified surrounding the human ferredoxin-encoding genes. Among them, one is located about 1000 bp upstream from the active gene, whereas two others flank the ferredoxin pseudogene, psi FDX3. All these Alu sequences contain poly(A) tails and are flanked by direct repeats, indicating that they arose by RNA- mediated transposition events.

Chernolovskaya, E. L., R. G. Borissov, A. V. Gorodjankin, E. M. Ivanova, N. D. Kobets, and V. V. Vlassov. 1991. Affinity modification of chromatin proteins located near open oligo(dA), oligo(dTG) and Alu-DNA sequences. Nucleic Acids Symp Ser. 24:312.

Chesnokov, I., V. Bozhkov, B. Popov, and N. Tomilin. 1991. Binding specificity of human nuclear protein interacting with the Alu- family DNA repeats. Biochem Biophys Res Commun. 178(2):613-9.

We have demonstrated earlier that human cells contain nuclear protein interacting with conserved GC-rich sequence motifs of human Alu-family DNA repeats. One of these sequences is located in the region between elements A and B of bipartite RNA polymerase III promoter of Alu (AB- region). In this study we have used a DNase I footprinting assay with an Alu restriction subfragment covering AB-region, as well as a gel mobility shift assay with appropriate synthetic oligonucleotides to analyse in more detail the interaction of the protein with AB-region. We have also used antibodies raised against a zinc-finger peptide to examine the presence of a zinc-finger in the Alu-binding protein. The results indicate that AGG triplets may be important for high-affinity binding of the protein to DNA, and that the Alu-binding protein is a zinc-finger protein.

Chung, B. C., and C. Y. Chang. 1991. Evolution of Alu repeats surrounding the human ferredoxin gene. Biochem Biophys Res Commun. 177(1):120-4.

Ferredoxin is an iron-sulfur protein that serves as an electron carrier for the mitochondrial oxidation/reduction system. During the characterization of the human ferredoxin gene, we have identified three Alu sequences surrounding it. When these Alu sequences were compared with others, all three of them are more related to the consensus Alu than the 7SL gene, the progenitor of the Alu family. It suggests that they are members of the modern Alu family. Their sequences differ from the Alu consensus sequence by about 5%, indicating that they were inserted into the chromosome about 35 million years ago.

Davidson, J. N., N. H. Khattar, and K. C. Chen. 1991. An unusual Alu repeat sequence within the CAD gene. J Mol Evol. 32(2):162-6.

There are several hundred thousand members of the Alu repeat family in the human genome. Those Alu elements sequenced to date appear to fit into subfamilies. A novel Alu has been found in an intron of the human CAD gene: it appears to be due to rearrangement between Alu repeats belonging to two different subfamilies. Further sequence data from this intron suggest that the Alu element may have rearranged prior to its entry into the CAD gene. Such findings indicate that, in addition to single nucleotide substitutions and deletions, DNA rearrangements may be a factor in generating the diversity of Alu repeats found in primate genomes.

Erickson, R. P., T. W. Glover, B. K. Hall, and M. Witt. 1991. Polymerase chain reactions with alphoid-repeat primers in combination with Alu or LINEs primers, generate chromosome-specific DNA fragments. Ann Hum Genet. 55(Pt 3):199-211.

Y alphoid primers in combination with Alu and LINEs primers generated new DNA fragments in polymerase chain reactions (PCR) on DNA from a Y- only somatic cell hybrid but not from X-only, 3-only, or 21-only hybrids. X alphoid primers used in a similar manner generated new DNA fragments from the X-only hybrid, and 1 of the primers (X2) also generated new DNA fragments on 3-only and 21-only hybrids when used in conjunction with Alu or LINEs primers. In all but one case, consensus alphoid primers generated new chromosome-specific fragments in PCR reactions with the Alu or LINEs primers. A search for cryptic Alu- or alphoid-alone PCR products as the source for one Alu-alphoid band (chosen at random) was negative. Partial sequencing of products demonstrated that alphoid and Alu sequences were indeed contiguous in some newly synthesized DNA fragments. While Alu or LINEs primers generate smears of DNA fragments on total human DNA, the alphoid-non- alphoid repeat combinations generated electrophoretically distinguishable bands of DNA when the template was total DNA. While these were distinguishable with different chromosome-specific alphoid primers, the DNA fragments were not of the same sizes as those generated with the chromosome-only hybrids.

Filatov, L. V., S. E. Mamayeva, and N. V. Tomilin. 1991. Alu family variations in neoplasia. Cancer Genet Cytogenet. 56(1):11-22.

Human chromosomes contain about one million copies of dispersed repeats of the Alu family which are distributed non-randomly. In this study we have compared the pattern of hybridization of tritiated Alu-probes on chromosomes of PHA-stimulated lymphocytes of normal donors and of non- stimulated bone marrow cells of acute leukemia patients, and found regular differences in this pattern over some chromosome bands (3q26, 8p11-p12, 14q24, 15q21, 6q22) between normal individuals and leukemia patients. These data were interpreted as indicative of somatic variation of the Alu family in acute leukemia. Possible mechanisms of the variation and the role of the Alu family in chromosome rearrangements in neoplasia are discussed.

Futreal, P. A., J. C. Barrett, and R. W. Wiseman. 1991. An Alu polymorphism intragenic to the TP53 gene. Nucleic Acids Res. 19(24):6977.

Guzzetta, V., R. Montes de Oca-Luna, J. R. Lupski, and P. I. Patel. 1991. Isolation of region-specific and polymorphic markers from chromosome 17 by restricted Alu polymerase chain reaction. Genomics. 9(1):31-6.

We demonstrate that the digestion of template DNAs with restriction endonucleases prior to Alu polymerase chain reaction ("restricted Alu- PCR") reduces the complexity of the Alu-primed amplification patterns of human DNA in somatic cell hybrids and allows a direct informative comparison of these patterns. A comparison of restricted Alu-PCR patterns of a monochromosomal hybrid retaining a human chromosome 17 (MH22-6) and a hybrid retaining a human chromosome 17 deleted for band p11.2 (DH110-D1) revealed four Alu-PCR products that were present in the former but absent in the latter hybrid. Hybridization of these fragments to the total Alu-PCR amplification products of the two hybrids confirmed their absence in DH110-D1 amplification products. Hybridization to a panel of somatic cell hybrids indicated that two of these fragments were deleted in the hybrid DH110-D1 and mapped to 17p11.2, as expected. However, two additional fragments were not deleted in the hybrid DH110-D1 and mapped to other regions of chromosome 17. An insertion-deletion polymorphism was associated with one of the latter fragments, which may be the mechanism for the lack of its amplification in the hybrid DH110-D1. Restricted Alu-PCR should enhance the applications of Alu-PCR and provides a new method for the identification of chromosome-specific polymorphic markers.

Jurka, J., and A. Milosavljevic. 1991. Reconstruction and analysis of human Alu genes. J Mol Evol. 32(2):105-21.

The existing classification of human Alu sequences is revised and expanded using a novel methodology and a larger set of sequence data. Our study confirms that there are two major Alu subfamilies, Alu-J and Alu-S. The Alu-S subfamily consists of at least five distinct subfamilies referred to as Alu-Sx, Alu-Sq, Alu-Sp, Alu-Sc, and Alu-Sb. The Alu-Sp and Alu-Sq subfamilies have been revealed by this study. Alu subfamilies differ from one another in a number of positions called diagnostic. In this paper the diagnostic positions are defined in quantitative terms and are used to evaluate statistical significance of the observed subfamilies. Each Alu subfamily most likely represents pseudogenes retroposed from evolving functional source Alu genes. Evidence presented in this paper indicates that Alu-Sp and Alu-Sc pseudogenes were retroposed from different source genes, during overlapping periods of time, and at different rates. Our analysis also indicates that the previously identified Alu-type transcript BC200 comes from an active Alu gene that might have existed even before the origin of dimeric Alu sequences. The source genes for Alu pseudogene families are reconstructed. It is assumed that diagnostic differences between reconstructed source genes reflect mutations that have occurred in true source Alu genes under natural selection. Some of these mutations are compensatory and are used to reconstruct a common secondary structure of Alu RNAs transcribed from the source genes. The biological function of Alu RNA is discussed in the context of its homology to the elongation-arresting domain of 7SL RNA.(ABSTRACT TRUNCATED AT 250 WORDS)

Jurka, J., and E. Zuckerkandl. 1991. Free left arms as precursor molecules in the evolution of Alu sequences. J Mol Evol. 33(1):49-56.

The dimeric Alu molecule of human and other primates is composed of a left and a right arm that are very similar but show characteristic differences. If the Alu sequence has arisen through the fusion of monomeric precursor molecules, the traces of such precursor genes are expected still to be present in contemporary primate DNA. We report finding seven independent human DNA sequences that qualify as descendants of a left-arm precursor gene. Some characteristics in primary and secondary structures of these sequences are described.

Lacerra, G., G. Fioretti, M. De Angioletti, L. Pagano, E. Guarino, C. de Bonis, A. Viola, G. Maglione, A. Scarallo, L. De Rosa, and et al. 1991. (Alpha)alpha 5.3: a novel alpha(+)-thalassemia deletion with the breakpoints in the alpha 2-globin gene and in close proximity to an Alu family repeat between the psi alpha 2- and psi alpha 1-globin genes. Blood. 78(10):2740-6.

A novel 5.3-kb deletion of the alpha-globin gene cluster was observed in a family from Naples, Southern Italy. It removes the 5' end of the alpha 2-globin gene, causing an alpha (+)-thalassemia defect. Because of the presence of the residual 3' end of the alpha 2-globin gene, we indicated this new haplotype with the symbol (alpha)alpha 5.3. The 5' breakpoint, the first to be reported in the intergene region of the psi alpha 2- and psi alpha 1-globin genes, is located 822 bp upstream of the cap site of the psi alpha 1-gene and about 150 bp upstream of a 300- nt Alu family member. The 3' breakpoint is located in the IVS-1 nt 58 of the alpha 2-globin gene. The 5.3-kb deleted fragment shows particular characteristics: it contains four Alu sequences having long regions 80% complementary and the 5'-GGCC-3' short repeat at both ends. The sequences spanning across the breakpoints on the same strand and containing this repeat on their 3' and 5' ends, respectively, are 17 of 25 base complementary. These particular features led us to assume the formation of a multistem-loop due to the intrastrand interaction between the complementary regions as intermediate to the deletion. The unusual localization of the 5' breakpoint suggests that even the intergene region of the psi alpha 2- and psi alpha 1-globin genes may function as a deletion target.

Ma, T. S., J. Ifegwu, L. Watts, M. J. Siciliano, R. Roberts, and M. B. Perryman. 1991. Serial Alu sequence transposition interrupting a human B creatine kinase pseudogene. Genomics. 10(2):390-9.

We have isolated, sequenced, and characterized a single-copy B creatine kinase pseudogene. The chromosomal assignment of this gene is 16p13 and a unique sequence probe from this locus detects EcoRI restriction fragment length polymorphisms of 7.8 and 5.4 kb. In 26 unrelated individuals, the frequencies for the 7.8- and 5.4-kb B creatine kinase pseudogene alleles were calculated to be 17.3 and 82.7%, respectively. The B creatine kinase pseudogene is interrupted by a 904-bp DNA insertion composed of three Alu repeat sequences in tandem flanked by an 18-bp direct repeat, derived from the pseudogene sequence. Nucleotide sequence analysis of the Alu elements suggests that the Alu sequences were incorporated into this locus in three separate integration events. Several complex clustered Alu repeat sequences without defined integration borders have been previously identified at different genomic loci. This is the first evidence that complex tandem Alu elements can integrate in an apparently serial manner in the human genome and supports the contention that Alu repeats integrate nonrandomly into the human genome.

Mitchell, G. A., D. Labuda, G. Fontaine, J. M. Saudubray, J. P. Bonnefont, S. Lyonnet, L. C. Brody, G. Steel, C. Obie, and D. Valle. 1991. Splice-mediated insertion of an Alu sequence inactivates ornithine delta-aminotransferase: a role for Alu elements in human mutation. Proc Natl Acad Sci U S A. 88(3):815-9.

In studies of mutations causing deficiency of ornithine delta- aminotransferase (EC 2.6.1.13), we found an allele whose mature mRNA has a 142-nucleotide insertion at the junction of sequences from exons 3 and 4. The insert derives from an Alu element in ornithine delta- aminotransferase intron 3 oriented in the direction opposite to transcription (an "antisense Alu"). A guanine----cytosine transversion creates a donor splice site in this Alu, activating a cryptic acceptor splice site at its 5' end and causing splice-mediated insertion of an Alu fragment into the mature ornithine-delta-aminotransferase mRNA. We note that the complement of the Alu consensus sequence has at least two cryptic acceptor sites and several potential donor sequences and predict that similar mutations will be found in other genes.

Muratani, K., T. Hada, Y. Yamamoto, T. Kaneko, Y. Shigeto, T. Ohue, J. Furuyama, and K. Higashino. 1991. Inactivation of the cholinesterase gene by Alu insertion: possible mechanism for human gene transposition. Proc Natl Acad Sci U S A. 88(24):11315-9.

The human cholinesterase (ChE) gene from a patient with acholinesterasemia was cloned and analyzed. By using ChE cDNA as a probe, four independent clones were isolated from a genomic library constructed from the patient's DNA. Sequencing analysis of all of the four clones revealed that exon 2 of the ChE gene was disrupted by a 342- base-pair (bp) insertion of Alu element, including a poly(A) tract of 38 bp, which showed 93% sequence homology with a current type of human Alu consensus sequence. Southern blot analysis showed that the Alu insertion occurred in both alleles of the patient and was inherited in the patient's family. This Alu insertion was flanked by 15-bp of target site duplication in exon 2 corresponding to positions 1062-1076 of ChE cDNA, indicating that an Alu element could have been integrated by retrotransposition. Thus, this case provides an important clue to the mechanism of inactivation of a gene by integration of a retrotransposon.

Nelson, D. L., A. Ballabio, M. F. Victoria, M. Pieretti, R. D. Bies, R. A. Gibbs, J. A. Maley, A. C. Chinault, T. D. Webster, and C. T. Caskey. 1991. Alu-primed polymerase chain reaction for regional assignment of 110 yeast artificial chromosome clones from the human X chromosome: identification of clones associated with a disease locus. Proc Natl Acad Sci U S A. 88(14):6157-61.

Over 400 yeast artificial chromosome (YAC) clones were isolated from the human X chromosome, and 110 of these were assigned to regions defined by chromosome translocation and deletion breakpoints. Polymerase chain reaction using Alu primers was applied to YAC clones in order to generate probes, to identify overlapping clones, and to derive "fingerprints" and sequence data directly from total yeast DNA. Several clones were identified in regions of medical interest. One set of three overlapping clones was found to cross a chromosomal translocation implicated in Lowe syndrome. The regional assignment of groups of YAC clones provides initiation points for further attempts to develop large cloned contiguous sequences, as well as material for investigation of regions involved in genetic diseases.

Sakamoto, K., C. M. Fordis, C. D. Corsico, T. H. Howard, and B. H. Howard. 1991. Modulation of HeLa cell growth by transfected 7SL RNA and Alu gene sequences. J Biol Chem. 266(5):3031-8.

Alu and 7SL RNA gene sequences were tested for the potential to regulate mammalian cell growth by introducing these sequences into HeLa cells in a coupled DEAE-dextran transfection/affinity cell sorting system. Both Alu and 7SL RNA genes mediated inhibition of [3H]thymidine and [35S]methionine incorporation in recipient cells. In addition, short term growth curves were performed on calcium phosphate/DNA cotransfected, affinity-purified cells. This second assay revealed that transfected Alu and 7SL RNA can also cause suppression of HeLa cell proliferation. To investigate whether transcription or polymerase III (pol III) transcription factor binding was required for inhibitory activity, mutations were introduced into RNA pol III B block promoter elements in each of these genes. Suppression of [3H]thymidine incorporation was dependent on the presence of this pol III element in both genes; likewise, 7SL RNA-mediated growth suppression required the presence of the pol III B block promoter element. The results of this study indicate that Alu and 7SL RNA gene sequences interact with cellular factors that are important for HeLa cell proliferation and suggest that these pol III-transcribed elements may be involved in the regulation of cellular growth.

Schmid, C. W. 1991. Human Alu subfamilies and their methylation revealed by blot hybridization. Nucleic Acids Res. 19(20):5613-7.

By a simple direct blot hybridization strategy, the existence of human Alu family subfamilies is confirmed. Using consensus restriction cleavage sites, individual bands can be resolved from genomic human DNA digests corresponding to three distinct Alu subfamilies. Digestion with methylation sensitive and insensitive restriction enzymes shows that the numerous CpG residues in the youngest Alu subfamilies are largely methylated in vivo, suggesting a model for the transcriptional regulation of Alu repeats.

Shaw, J. P., J. Marks, and C. K. Shen. 1991. The adult alpha-globin locus of Old World monkeys: an abrupt breakdown of sequence similarity to human is defined by an Alu family repeat insertion site. J Mol Evol. 33(6):506-13.

The haploid genomes of all known primates have two or more adult alpha- globin genes contained within tandemly arranged duplication units. Although the tandem duplication event generating these alpha-globin loci is believed to occur prior to the divergence of primates, a number of length polymorphisms exist within the loci among different primate species. In order to understand the molecular basis of these length polymorphisms, we have cloned and determined the nucleotide sequence of a major portion of the rhesus monkey adult alpha-globin locus. Sequence comparison to human suggests that the length difference between the adult alpha-globin loci of human and Old World monkey is the result of one or more DNA recombination processes, all of which appeared to be related to the transposition of Alu family repeats. First, the finding of a monomeric Alu family repeat at the junction between nonhomology block I and homology block Y of the alpha 2 gene-containing unit in rhesus macaque suggests that the dimeric Alu family repeat, Alu 3, at the orthologous position in human was generated by insertion of a monomeric Alu family repeat into the 3' end of another preexisting Alu family repeat. Second, two Alu family repeats, Alu 1 and Alu 2, exist in human at the 3' end of each of the two X homology blocks, respectively. However, this pair of paralogous Alu family repeats is absent at the corresponding positions in rhesus macaques. This raises interesting questions regarding the evolutionary origin of Alu 1 and Alu 2. Finally, DNA sequences immediately downstream from the insertion site of Alu 2 are completely different between human and rhesus macaque.(ABSTRACT TRUNCATED AT 250 WORDS)

Shen, M. R., M. A. Batzer, and P. L. Deininger. 1991. Evolution of the master Alu gene(s). J Mol Evol. 33(4):311-20.

A comparison of Alu sequences that comprise more recently amplified Alu subfamilies was made. There are 18 individual diagnostic mutations associated with the different subfamilies. This analysis confirmed that the formation of each subfamily can be explained by the sequential accumulation of mutations relative to the previous subfamily. Polymerase chain reaction amplification of orthologous loci in several primate species allowed us to determine the time of insertion of Alu sequences in individual loci. These data suggest that the vast majority of Alu elements amplified at any given time comprised a single Alu subfamily. We find that, although the individual divergence relative to a consensus sequence correlate reasonably well with sequence age, the diagnostic mutations are a more accurate measure of the age of any individual Alu family member. Our data are consistent with a model in which all Alu family members have been made from a single master gene or from a series of sequential master genes. This master gene(s) accumulated diagnostic base changes, resulting in the amplification of different subfamilies from the master gene at different times in primate evolution. The changes in the master gene(s) probably occurred individually, but their appearance is clearly punctuated. Ten of them have occurred within an approximately 15-million-year time span, 40-25 million years ago, and 8 changes have occurred within the last 5 million years. Surprisingly, no changes appeared in the 20 million years separating these periods.

Sinnett, D., C. Richer, J. M. Deragon, and D. Labuda. 1991. Alu RNA secondary structure consists of two independent 7 SL RNA-like folding units. J Biol Chem. 266(14):8675-8.

The amplification of genomic Alu elements by retroposition, i.e. by reintegration of reverse-transcribed RNA, suggests that Alu RNA plays an important role in this process. We report enzymatic studies of the secondary structure of Alu RNAs transcribed in vitro from two recently retroposed Alu elements. These experiments show that the dimeric organization of an Alu sequence is reflected in its RNA folding. Alu subunits fold independently, conserving secondary structure motifs of their progenitor 7 SL RNA molecule. Energy minimization analysis indicates that this folding pattern is also characteristic of different Alu and Alu-like sequences and has been conserved since primate divergence. By analogy to 7 SL RNA, the Alu RNA folding may be important for specific interactions with proteins. This could indicate a physiological function for Alu transcripts. However, this can be also seen as a structural adaptation leading to efficient retroposition of these sequence elements.

Strub, K., J. Moss, and P. Walter. 1991. Binding sites of the 9- and 14-kilodalton heterodimeric protein subunit of the signal recognition particle (SRP) are contained exclusively in the Alu domain of SRP RNA and contain a sequence motif that is conserved in evolution. Mol Cell Biol. 11(8):3949-59.

The mammalian signal recognition particle (SRP) is a small cytoplasmic ribonucleoprotein required for the cotranslational targeting of secretory proteins to the endoplasmic reticulum membrane. The heterodimeric protein subunit SRP9/14 was previously shown to be essential for SRP to cause pausing in the elongation of secretory protein translation. RNase protection and filter binding experiments have shown that binding of SRP9/14 to SRP RNA depends solely on sequences located in a domain of SRP RNA that is strongly homologous to the Alu family of repetitive DNA sequences. In addition, the use of hydroxyl radicals, as RNA-cleaving reagents, has revealed four distinct regions in this domain that are in close contact with SRP9/14. Surprisingly, the nucleotide sequence in one of these contact sites, predicted to be mostly single stranded, was found to be extremely conserved in SRP RNAs of evolutionarily distant organisms ranging from eubacteria and archaebacteria to yeasts and higher eucaryotic cells. This finding suggests that SRP9/14 homologs may also exist in these organisms, where they possibly contribute to the regulation of protein synthesis similar to that observed for mammalian SRP in vitro.

Wallace, M. R., L. B. Andersen, A. M. Saulino, P. E. Gregory, T. W. Glover, and F. S. Collins. 1991. A de novo Alu insertion results in neurofibromatosis type 1. Nature. 353(6347):864-6.

Neurofibromatosis type 1 (NF1) is a common autosomal dominant disorder with a high mutation rate and variable expression, characterized by neurofibromas, cafe-au-lait spots, Lisch nodules of the iris, and less frequent features including bone deformities and learning disabilities. The recently cloned NF1 gene encodes a transcript of 13 kilobases from a ubiquitously expressed locus on chromosome 17. Most NF1 patients are expected to have unique mutations, but only a few have so far been characterized, restricting genetic and functional information and the design of DNA diagnostics. We report an unusual NF1 mutation, that of a de novo Alu repetitive element insertion into an intron, which results in deletion of the downstream exon during splicing and consequently shifts the reading frame. This previously undescribed mechanism of mutation indicates that Alu retrotransposition is an ongoing process in the human germ line.

Xu, G. F., L. Nelson, P. O'Connell, and R. White. 1991. An Alu polymorphism intragenic to the neurofibromatosis type 1 gene (NF1). Nucleic Acids Res. 19(13):3764.

Batzer, M. A., and P. L. Deininger. 1991. A human-specific subfamily of Alu sequences. Genomics. 9(3):481-7.

Of a total of 500,000 Alu family members, approximately 500 are present as a human-specific (HS) subfamily. Each of the HS subfamily members shares a high degree of nucleotide identity and is not present at orthologous positions in other primate genomes, suggesting that HS subfamily members have recently inserted within the human genome. This confirms the hypothesis that the majority of Alu family members are amplified copies of a "master" gene(s). This master gene appears to be amplifying at a rate much slower than that seen earlier in primate evolution. Some of the HS Alu subfamily members have amplified so recently that they are dimorphic in the human population, making them a potentially powerful tool for studies of human populations.

Bancroft, J. D., L. A. Schaefer, and S. J. Degen. 1990. Characterization of the Alu-rich 5'-flanking region of the human prothrombin-encoding gene: identification of a positive cis-acting element that regulates liver-specific expression. Gene. 95(2):253-60.

The nt sequence of 6127 bp of sequence upstream of the human prothrombin-encoding gene (F2) has been determined. Since we previously characterized 417 bp of DNA immediately upstream from the transcription start point (tsp), 6544 bp of continuous flanking sequence are known. Eleven Alu repeat sequences present in this region comprise 45% of the sequence; other repetitive sequences were identified by searching GenBank. The tsp was found to be heterogeneous by exon mapping and primer extension analysis. To localize the cis-acting sequences responsible for the liver-specific expression of F2, hybrid cat genes were constructed with various lengths of F2 5'-flanking region cloned upstream from a promoterless cat gene. After transfection into HepG2 and HeLa cells, it was inferred that the region between nt -1101 and - 798 was required for synthesis in HepG2 cells; no synthesis was observed using these constructs in HeLa cells. Two sequences for known liver-specific or regulatory cis-acting sequences were identified in this region.

Batzer, M. A., G. E. Kilroy, P. E. Richard, T. H. Shaikh, T. D. Desselle, C. L. Hoppens, and P. L. Deininger. 1990. Structure and variability of recently inserted Alu family members [published erratum appears in Nucleic Acids Res 1991 Feb 11;19(3):698-9]. Nucleic Acids Res. 18(23):6793-8.

The HS subfamily of Alu sequences is comprised of a group of nearly identical members. Individual subfamily members share 97.7% nucleotide identity with each other and 98.9% nucleotide identity with the HS consensus sequence. Individual subfamily members are on the average 2.8 million years old, and were probably derived from a single source 'master' gene sometime after the human/great ape divergence. The recent Alu family member insertions provide a better image of the structure of Alu retroposons before they have had the opportunity to change significantly. All of the HS subfamily members are flanked by perfect direct repeats as a result of insertion at staggered nicks. The 'master' gene from which the HS subfamily members were derived had an oligo-dA rich tail at least 40 bases long. The 'master' gene is very rich in CpG dinucleotides, but nucleotide substitutions within subfamily members accumulated in a random manner typical for Alu sequence with CpG substitutions occurring 9.2 fold faster than non-CpG substitutions.

Devlin, R. H., S. Deeb, J. Brunzell, and M. R. Hayden. 1990. Partial gene duplication involving exon-Alu interchange results in lipoprotein lipase deficiency. Am J Hum Genet. 46(1):112-9.

Major structural rearrangements are uncommon causes of mutation in human genetic diseases. We have previously described that a significant proportion of unrelated patients of western European descent who are deficient in lipoprotein lipase (LPL) activity have a major structural rearrangement in the LPL gene. Here we report the detailed characterization of this mutation. We show that this rearrangement is due to a duplication of approximately 2 kb which results from juxtaposition of intron 6 to a partially duplicated exon 6. We have sequenced both the junction fragment of this duplication and the corresponding wild-type regions and have found that the breakpoint in intron 6 is associated with the simple repeat found at the 3' end of an Alu element. The breakpoint within exon 6 shows no homology to this simple repeat. This result both suggests that this interchange arose as a nonhomologous recombination event and shows that such events resulting in duplication which occur in normal gene evolution may also lead to genetic disease. Cloning of the junction fragment has allowed synthesis of appropriate primers for rapid screening for this rearrangement in other families with LPL deficiency.

Economou, E. P., A. W. Bergen, A. C. Warren, and S. E. Antonarakis. 1990. The polydeoxyadenylate tract of Alu repetitive elements is polymorphic in the human genome. Proc Natl Acad Sci U S A. 87(8):2951-4.

To identify DNA polymorphisms that are abundant in the human genome and are detectable by polymerase chain reaction amplification of genomic DNA, we tested the hypothesis that the polydeoxyadenylate tract of the Alu family of repetitive elements is polymorphic among human chromosomes. We analyzed the 3' ends of three specific Alu sequences and found that two (in the adenosine deaminase gene and the beta-globin pseudogene) were polymorphic. This novel class of polymorphisms, termed AluVpA [Alu variable poly(A)] may represent one of the most useful and informative group of DNA markers in the human genome.

Epstein, N., O. Nahor, and J. Silver. 1990. The 3' ends of alu repeats are highly polymorphic. Nucleic Acids Res. 18(15):4634.

Gonzalez-Crespo, S., M. Monfar, and A. Boronat. 1990. The proximal 5'-flanking region of the gene encoding human growth hormone-releasing factor contains an inserted Alu sequence. Gene. 93(2):321-2.

Howard, B. H., and K. Sakamoto. 1990. Alu interspersed repeats: selfish DNA or a functional gene family? New Biol. 2(9):759-70.

Within the genomes of higher eukaryotic cells, short interspersed repetitive sequences appear to be ubiquitous, but also remarkably varied with respect to copy number and position. Many of these repeat families, including the human Alu family, can be transcribed by RNA polymerase III, and evidence has accumulated from a variety of sources that levels of repeat transcripts whose transcription is dependent on RNA polymerase III are sensitive to cellular transformation as well as changes in differentiation state. Although interspersed repetitive sequences have in the past been dismissed as nonfunctional, the discovery of the linkage to differentiation state, as well as other recent developments, suggest that the question of repeat sequence functionality should be reexamined.

Kornreich, R., D. F. Bishop, and R. J. Desnick. 1990. Alpha-galactosidase A gene rearrangements causing Fabry disease. Identification of short direct repeats at breakpoints in an Alu-rich gene. J Biol Chem. 265(16):9319-26.

Fabry disease, an inborn error of glycosphingolipid catabolism, results from mutations in the X-linked gene encoding the lysosomal enzyme, alpha-galactosidase A (EC 3.2.1.22). Six alpha-galactosidase A gene rearrangements that cause Fabry disease were investigated to assess the role of Alu repetitive elements and short direct and/or inverted repeats in the generation of these germinal mutations. The breakpoints of five partial gene deletions and one partial gene duplication were determined by either cloning and sequencing the mutant gene from an affected hemizygote, or by polymerase chain reaction amplifying and sequencing the genomic region containing the novel junction. Although the alpha-galactosidase A gene contains 12 Alu repetitive elements (representing approximately 30% of the 12-kilobase (kb) gene or approximately 1 Alu/1.0 kb), only one deletion resulted from an Alu-Alu recombination. The remaining five rearrangements involved illegitimate recombinational events between short direct repeats of 2 to 6 base pairs (bp) at the deletion or duplication breakpoints. Of these rearrangements, one had a 3' short direct repeat within an Alu element, while another was unusual having two deletions of 1.7 kb and 14 bp separated by a 151-bp inverted sequence. These findings suggested that slipped mispairing or intrachromosomal exchanges involving short direct repeats were responsible for the generation of most of these gene rearrangements. There were no inverted repeat sequences or alternating purine-pyrimidine regions which may have predisposed the gene to these rearrangements. Intriguingly, the tetranucleotide CCAG and the trinucleotide CAG (or their respective complements, CTGG and CTG) occurred within or adjacent to the direct repeats at the 5' breakpoints in three and four of the five alpha-galactosidase A gene rearrangements, respectively, suggesting a possible functional role in these illegitimate recombinational events. These studies indicate that short direct repeats are important in the formation of gene rearrangements, even in human genes like alpha-galactosidase A that are rich in Alu repetitive elements.

Korotkov, E. V. 1990. [Alu-like sequences in the regions of replication initiation in plasmids p15A and R6K]. Izv Akad Nauk SSSR [Biol](3):359-65.

A method of computer analysis of DNA sequences has been proposed. It is based on information similarity of compared sequences and it significantly increases the usefulness of the computer analysis. This approach has been applied to the search of interconnected areas of Alu- repeats and replication origins of p15A and R6K plasmids. An Alu-like region located in the first stem of the secondary structure of RNA-1 and E. coli RNA-polymerase binding site has been found in the p15A. On R6K replication origin, Alu-like repeats have been found in the area of tandem 22 bp repeats. This comparison also allowed to reveal hidden periodicity of the sequence of human Alu-repeat. A hypothesis that explained the data obtained has been proposed. The proposed approach may be used as a method for revealing DNA sequences that have similar genetic functions.

Matera, A. G., U. Hellmann, M. F. Hintz, and C. W. Schmid. 1990. Recently transposed Alu repeats result from multiple source genes. Nucleic Acids Res. 18(20):6019-23.

A human Alu repeat subfamily (the PV subfamily) whose members include insertional polymorphisms is found, as predicted, to differ by five tightly linked mutations relative to another subfamily of recently inserted Alu repeats. Based on these sequence differences some of the small number of polymorphic Alus can be selected from the background of nearly one million member sequences which are fixed in the human genome. Shared patterns of mutations suggest that PV subfamily members are the progeny of several different founder sequences. The additional observation that all members of the PV subfamily end in a stretch of uninterrupted polyadenine residues rather than merely A-rich sequences is evidence for post-transcriptional polyadenylation of the presumptive RNA intermediate. The drift of polyadenine sequences toward tandemly repeated A-rich motifs suggests a biological function that may select for the fixation of dispersed Alu repeats.

Matera, A. G., U. Hellmann, and C. W. Schmid. 1990. A transpositionally and transcriptionally competent Alu subfamily. Mol Cell Biol. 10(10):5424-32.

DNA base sequence comparisons indicate that a subfamily of recently transposed human Alu repeats are distinguished from most Alu repeats by diagnostic sequence differences. Using an oligonucleotide hybridization probe that incorporates these sequence features, we found that there was an expansion of this Alu subfamily following the divergence of humans and African apes. This oligonucleotide was used to select human genomic clones containing representatives of this subfamily. One representative member of this subfamily was evidently absent from the corresponding chimpanzee locus and was associated with a restriction fragment length polymorphism in the human genome. This apparently polymorphic member had all the diagnostic sequence features that initially predicted the existence of a newly expanding Alu subfamily. A transpositionally active sequence variant should also be transcriptionally active in at least some cell types or tissues. Northern (RNA) blot hybridization, primer extension, and RNA sequence analysis demonstrated the existence of different-length polyadenylated and nonpolyadenylated transcripts corresponding to this subfamily. Evidence for 3' processing and subcellular localization of these transcripts is discussed. Most of the nearly one million human Alu repeats are pseudogenes with respect to coding for either an RNA product or new family members; a select and identifiable subset of Alu repeats serve as transcriptionally and transpositionally competent source genes.

Merritt, C. M., S. Easteal, and P. G. Board. 1990. Evolution of human alpha 1-acid glycoprotein genes and surrounding Alu repeats. Genomics. 6(4):659-65.

There is a mosaic pattern of variation between the two tandemly arranged human alpha 1-acid glycoprotein genes. Both the synonymous and the nonsynonymous sites of exons 3 and 4 are more divergent than the rest of the gene, suggesting that they have had a different evolutionary history. Comparisons of the two gene sequences with rat AGP indicate that exons 3 and 4 of AGP2 have been evolving without functional constraint since their divergence from AGP1. It is proposed that the conserved region of the gene has been homogenized recently by gene conversion with the homologous regions of AGP1. The Alu sequences surrounding the genes appear to have been involved in both the gene duplication and the gene conversion events.

Neote, K., B. McInnes, D. J. Mahuran, and R. A. Gravel. 1990. Structure and distribution of an Alu-type deletion mutation in Sandhoff disease. J Clin Invest. 86(5):1524-31.

Sandhoff disease is a recessively inherited lysosomal storage disease resulting from a deficiency of beta-hexosaminidase activity. The enzyme occurs in two major forms, beta-hexosaminidase A, composed of an alpha- and beta-subunit and beta-hexosaminidase B, composed of two beta- subunits. Both isozyme activities are deficient in Sandhoff disease, owing to mutations of the HEXB gene encoding the common beta-subunit. We have cloned and fully characterized a deletion at the HEXB gene from fibroblasts of a patient with the infantile form of Sandhoff disease. The deletion removes approximately 16 kb of DNA including the HEXB promoter, exons 1-5 and part of intron 5. It most likely arose from recombination between two Alu sequences, with the breakpoints occurring at the midpoint between the left and right arms in each case and regenerating an intact Alu element in the deletion sequence. The deletion allele accounts for 27% of the Sandhoff mutant alleles we analyzed. Two cell lines were shown to be homozygous for the deletion and both had the infantile form of the disease. Four additional patients were compound heterozygotes with other mutations, all of whom displayed a different clinical phenotype. Finally, the mutant allele was present in different ethnic backgrounds, suggesting that it may have been subject to genetic drift.

Okada, N. 1990. Transfer RNA-like structure of the human Alu family: implications of its generation mechanism and possible functions. J Mol Evol. 31(6):500-10.

Structural resemblance of the human Alu family with a subset of vertebrate tRNAs was detected. Of four tRNAs, tRNA(Lys), tRNA(Ile), tRNA(Thr), and tRNA(Tyr), which comprise a structurally related family, tRNA(Lys) is the most similar to the human Alu family. Of the 76 nucleotides in lysine tRNA (including the CCA tail), 47 are similar to the human Alu family (60% identity). The secondary structure of the human Alu family corresponding to the D-stem and anticodon stem regions of the tRNA appears to be very stable. The 7SL RNA, which is a progenitor of the human Alu family, is less similar to lysine tRNA (55% identity), and the secondary structure of the 7SL RNA folded like a tRNA is less stable than that of the human Alu family folded likewise. Insertion of the tetranucleotide GAGA, which is an important region of the second promoter for RNA polymerase III in the Alu sequence, occurred during the deletion and ligation process to generate the Alu sequence from the parental 7SL RNA. These results suggest that the human Alu family was generated from the 7SL RNA by deletion, insertion, and mutations, which thus modified the ancestral 7SL sequence so that it could form a structure more closely resembling lysine tRNA. The similarities of several short interspersed sequences to the lysine tRNA were also examined. The Galago type 2 family, which was reported to be derived from a methionine initiator tRNA, was also found to be similar to the lysine tRNA. Thus lysine tRNA-like structures are widespread in genomes in the animal kingdom. The implications of these findings in relation to the mechanism of generation of the human Alu family and its possible functions are discussed.

Orita, M., T. Sekiya, and K. Hayashi. 1990. DNA sequence polymorphisms in Alu repeats. Genomics. 8(2):271-8.

We have developed an efficient method for detection of sequence differences in genomic DNA based on a new principle (M. Orita et al., 1989, Genomics 5: 874-879). Using this method, we show here that approximately half the Alu repeats interspersed in the human genome are significantly polymorphic. Analysis of Alu repeat polymorphism should be useful in construction of a high-resolution map and also in identifying genotypes of individuals for clinical and other purposes because the repeats are ubiquitous and the technique for their detection is simple.

Smidt, M., I. Kirsch, and L. Ratner. 1990. Deletion of Alu sequences in the fifth c-sis intron in individuals with meningiomas. J Clin Invest. 86(4):1151-7.

An abnormality in the c-sis protooncogene was identified in leukocyte DNA from members of a family predisposed to the development of meningioma, and was found to be associated with the development of the tumor in those individuals. Molecular analysis of this abnormality demonstrated a deletion within the fifth intron of the c-sis gene. The normal c-sis gene has an Alu sequence in this region which includes two perfect 130 nucleotide repeated sequences separated by 5 bp. The deleted c-sis allele is missing precisely one copy of the 130 bp repeat and the intervening 5 bp. An identical deletion was also found in DNA from 1 of 13 sporadic meningiomas.

Stoppa-Lyonnet, D., P. E. Carter, T. Meo, and M. Tosi. 1990. Clusters of intragenic Alu repeats predispose the human C1 inhibitor locus to deleterious rearrangements. Proc Natl Acad Sci U S A. 87(4):1551-5.

Frequent alterations in the structure of the complement component C1 inhibitor gene have been found in patients affected by the common variant of hereditary angioedema, characterized by low plasma levels of C1 inhibitor. This control protein limits the enzymic activity of the first component of complement and of other plasma serine proteases. Sequence comparisons of a 4.6-kilobase-long segment of the normal gene and the corresponding gene segments isolated from two patients carrying family-specific DNA deletions point to unusually long clusters of tandem repeats of the Alu sequence family as a source of genetic instability in this locus. Unequal crossovers, in a variety of registers, among Alu sequences of the clusters result in deletions of variable length that encompass exon 4. In a third family, exon 4 was instead found to be duplicated along with the same tracts of flanking introns lost in one of the deletions. In addition to undergoing Alu- mediated partial deletions and duplications, the gene is also a target for more recent retroposition events. Gross alterations in the C1 inhibitor gene account for about 20% of the hereditary angioedema chromosomes and consequently make this gene a prime example of the mutagenic liability of Alu repeats.

Strub, K., and P. Walter. 1990. Assembly of the Alu domain of the signal recognition particle (SRP): dimerization of the two protein components is required for efficient binding to SRP RNA. Mol Cell Biol. 10(2):777-84.

The signal recognition particle (SRP), a cytoplasmic ribonucleoprotein, plays an essential role in targeting secretory proteins to the rough endoplasmic reticulum membrane. In addition to the targeting function, SRP contains an elongation arrest or pausing function. This function is carried out by the Alu domain, which consists of two proteins, SRP9 and SRP14, and the portion of SRP (7SL) RNA which is homologous to the Alu family of repetitive sequences. To study the assembly pathway of the components in the Alu domain, we have isolated a cDNA clone of SRP9, in addition to a previously obtained cDNA clone of SRP14. We show that neither SRP9 nor SRP14 alone interacts specifically with SRP RNA. Rather, the presence of both proteins is required for the formation of a stable RNA-protein complex. Furthermore, heterodimerization of SRP9 and SRP14 occurs in the absence of SRP RNA. Since a partially reconstituted SRP lacking SRP9 and SRP14 [SRP(-9/14)] is deficient in the elongation arrest function, it follows from our results that both proteins are required to assemble a functional domain. In addition, SRP9 and SRP14 synthesized in vitro from synthetic mRNAs derived from their cDNA clones restore elongation arrest activity to SRP(-9/14).

Tomilin, N. V., S. M. Iguchi-Ariga, and H. Ariga. 1990. Transcription and replication silencer element is present within conserved region of human Alu repeats interacting with nuclear protein. FEBS Lett. 263(1):69-72.

Human cells contain a nuclear protein interacting with Alu repeats, and this protein seems to recognize a conserved sequence motif, GGAGGC, present within the RNA polymerase III promoter and within the SV40 T- antigen-dependent ARS-like element. To study the potential functional role of this element, we have inserted the sequence into a chloramphenicolacetyltransferase (CAT) expression vector with a SV40 promoter and enhancer element from the up-stream region of the human c- myc gene, and transfected HeLa cells with the resulting plasmid. Analysis of expression by the CAT assay indicates that the Alu-derived sequence supresses transcription of the CAT gene driven by the c-myc enhancer/SV40 promoter. The Alu-derived sequence also inhibits ARS activity of the c-myc enhancer. The data allow the explanation of the transcriptional inactivity of Alu repeats in HeLa cells, and suggest the existence of a negative control of Alu transcription.

Vnencak-Jones, C. L., and J. A. d. Phillips. 1990. Hot spots for growth hormone gene deletions in homologous regions outside of Alu repeats. Science. 250(4988):1745-8.

Familial growth hormone deficiency type 1A is an autosomal recessive disease caused by deletion of both growth hormone-1 (GH1) alleles. Ten patients from heterogeneous geographic origins showed differences in restriction fragment length polymorphism haplotypes in nondeleted regions that flanked GH1, suggesting that these deletions arose from independent unequal recombination events. Deoxyribonucleic acid (DNA) samples from nine of ten patients showed that crossovers occurred within 99% homologous, 594-base pair (bp) segments that flanked GH1. A DNA sample from one patient indicated that the crossover occurred within 454-bp segments that flanked GH1 and contained 274-bp repeats that are 98% homologous. Although Alu repeats, which are frequent sites of recombination, are adjacent to GH1, they were not involved in any of the recombination events studied. These results suggest that length and degree of DNA sequence homology are important in defining recombination sites that resulted in GH1 deletions.

Wu, J., G. J. Grindlay, P. Bushel, L. Mendelsohn, and M. Allan. 1990. Negative regulation of the human epsilon-globin gene by transcriptional interference: role of an Alu repetitive element. Mol Cell Biol. 10(3):1209-16.

The human epsilon-globin gene has a number of alternative transcription initiation sites which correspond with regions of DNase I hypersensitivity upstream of the canonical cap site. Transcripts originating from the promoters located -4.3/-4.5 and -1.48 kilobase pairs (kbp) and -900 and -200 base pairs (bp) upstream of the major epsilon-globin cap site can, at certain stages of erythroid differentiation, extend through the gene and are polyadenylated. The 350-bp PolIII transcripts, originating within the Alu repetitive element -2.2 kbp upstream of the cap site, extend in the opposite direction from the gene, are nonpolyadenylated, nucleus confined, and are detectable only in mature K562 cells or mature embryonic red blood cells where the epsilon-globin major cap site is maximally transcribed. Fragments containing the promoters located between -4.5 and -4.3 kbp upstream of the gene down regulate transcription from the epsilon- globin gene 20- to 30-fold in a transient expression assay in which both erythroid and nonerythroid cell lines were used. This occurs only when the direction of transcription from the -4.3/-4.5-kbp promoters is towards the gene, and we hypothesize that down regulation is caused by transcriptional interference. Fragments containing the Alu repetitive element -2.2 kbp upstream of the gene can overcome down regulation of the epsilon-globin gene by the -4.5-kbp element when interposed in the direct orientation between this element and the epsilon-globin gene.

Zuliani, G., and H. H. Hobbs. 1990. A high frequency of length polymorphisms in repeated sequences adjacent to Alu sequences. Am J Hum Genet. 46(5):963-9.

We describe a new class of DNA length polymorphism that is due to a variation in the number of tandem repeats associated with Alu sequences (Alu sequence-related polymorphisms). The polymerase chain reaction was used to selectively amplify a (TTA)n repeat identified in the 3-hydroxy- 3-methylglutaryl coenzyme A (HMG CoA) reductase gene from genomic DNA of 41 human subjects, and the size of the amplified products was determined by gel electrophoresis. Seven alleles were found that differed in size by integrals of three nucleotides. The allele frequencies ranged from 1.5% to 52%, and the overall heterozygosity index was 62%. The polymorphic TTA repeat was located adjacent to a repetitive sequence of the Alu family. A homology search of human genomic DNA sequences for the trinucleotide TTA (at least five members in length) revealed tandem repeats in six other genes. Three of the six (TTA)n repeats were located adjacent to Alu sequences, and two of the three (in the genes for beta-tubulin and interleukin-1 alpha) were found to be polymorphic in length. Tandemly repetitive sequences found in association with Alu sequences may be frequent sites of length polymorphism that can be used as genetic markers for gene mapping or linkage analysis.

Ariga, T., P. E. Carter, and A. E. d. Davis. 1990. Recombinations between Alu repeat sequences that result in partial deletions within the C1 inhibitor gene. Genomics. 8(4):607-13.

Genomic DNA sequence analysis was used to define the extent of deletions within the C1 inhibitor gene in two families with type I hereditary angioneurotic edema. Southern blot analysis initially indicated the presence of the partial deletions. One deletion was approximately 2 kb and included exon VII, whereas the other was approximately 8.5 kb and included exons IV-VI. Genomic libraries from an affected member of each family were constructed and clones containing the deletions were analyzed. Sequence analysis of the deletion joints of the mutants and corresponding regions of the normal gene in the two families demonstrated that both deletion joints resulted from recombination of two Alu repetitive DNA elements. Alu repeat sequences from introns VI and VII combined to make a novel Alu in family A, and Alu sequences in introns III and VI were spliced to make a new Alu in family B. The splice sites in the Alu sequences of both mutants were located in the left arm of the Alu element, and both recombination joints overlapped one of the RNA polymerase III promoter sequences. Because the involved Alu sequences, in both instances, were oriented in the same direction, unequal crossingover is the most likely mechanism to account for these mutations.

Brownell, E., N. Mittereder, and N. R. Rice. 1989. A human rel proto-oncogene cDNA containing an Alu fragment as a potential coding exon. Oncogene. 4(7):935-42.

Two rel-containing cDNA clones were isolated from a library derived from the Daudi human cell line, which is known to express c-rel mRNA. Clone #1 appeared to contain the entire c-rel coding sequence, which differs from v-rel in having three additional N-terminal residues and 111 additional C-terminal residues. In addition, Clone #1 had an internal 32 amino acid exon not found in v-rel or in turkey c-rel. Clone #2 was truncated at its 5' end and did not contain this new exon. Analysis of a genomic clone of human c-rel revealed that the new exon was a portion of an inverted Alu repeat. The occurrence of potential splice sites and of open reading frames in the inverted consensus Alu sequence suggests that the incorporation of Alu fragments as potential coding exons could be a relatively common event in human mRNAs. Whether such messages can be translated is unknown: antiserum raised against a peptide at the predicted C-terminus of the c-rel protein precipitated p82hc-rel, but antiserum raised against a peptide located in the Alu exon did not.

Chen, S. J., Z. Chen, L. d'Auriol, M. Le Coniat, D. Grausz, and R. Berger. 1989. Ph1+bcr- acute leukemias: implication of Alu sequences in a chromosomal translocation occurring in the new cluster region within the BCR gene. Oncogene. 4(2):195-202.

Chromosomal breakpoints on chromosome 22 are located in the first intron of the bcr gene in half of the Philadelphia-positive acute leukemias (Ph1+bcr- AL). We have previously shown that, in these cases, the breakpoints are clustered in the 3' portion of the bcr gene first intron, particularly in a region called bcr2 or m-bcr-1. In order to search for mechanisms underlying the reciprocal chromosome translocation, molecular analysis of breakpoints on chromosome 9 and 22 were performed in a Ph1+bcr- acute lymphoblastic leukemia with bcr2 rearrangement. The comparison of rearranged sequences with their normal counterparts showed that human repetitive Alu sequences were physically linked to the translocation on both chromosomes. In addition an inverted Alu repeat was found 5' to each rearranged Alu sequence on chromosome 22 and 9, with an intervening sequence of 210 and 90bp respectively. This allows to propose a new model, still to be confirmed, of recombination after formation of two hairpin structures which could facilitate the genesis of the chromosomal accident.

Chen, S. J., Z. Chen, M. P. Font, L. d'Auriol, C. J. Larsen, and R. Berger. 1989. Structural alterations of the BCR and ABL genes in Ph1 positive acute leukemias with rearrangements in the BCR gene first intron: further evidence implicating Alu sequences in the chromosome translocation. Nucleic Acids Res. 17(19):7631-42.

In the Philadelphia positive bcr negative acute leukemias (Ph1+bcr- AL), the chromosomal breakpoints on chromosome 22 have been shown clustered within 10.8kb (bcr2) and 5kb (bcr3) fragments of the first intron of the BCR gene. We previously reported that the breakpoints were localized in Alu repeats on chromosomes 9 and 22 in a Ph1+bcr- acute lymphoblastic leukemia with a rearrangement involving bcr2. Molecular data of two other Ph1 translocations, one a Ph1+bcr- acute myeloblastic leukemia in the bcr2 region, and the other an acute lymphoblastic leukemia in the bcr3 region are presented. In the former, the breakpoints on chromosomes 9 and 22 are localized in Alu repeats, in regions with two inverted Alu sequences, as in our previously reported case. In the second leukemia, the breakpoints are not located in Alu sequences, but such repeats are found in their vicinity. The implications of these findings are discussed.

Ellis, N. A., P. J. Goodfellow, B. Pym, M. Smith, M. Palmer, A. M. Frischauf, and P. N. Goodfellow. 1989. The pseudoautosomal boundary in man is defined by an Alu repeat sequence inserted on the Y chromosome. Nature. 337(6202):81-4.

The Y chromosome, which in man determines the male sex, is composed of two functionally distinct regions. The pseudoautosomal region is shared between the X and Y chromosome and is probably required for the correct segregation of the sex chromosomes during male meiosis. The second region includes the sex-determining gene(s), the presence of which is necessary for the development of testes. The two regions have contrasting genetic properties: the pseudoautosomal region recombines between the X and Y chromosome; the Y-specific region must avoid recombination otherwise the chromosomal basis of sex-determination breaks down. The pseudoautosomal region is bounded at the distal end by the telomere and at the proximal end by X- and Y-specific DNA. We have found that the proximal boundary was formed by the insertion of an Alu sequence on the Y chromosome early in the primate lineage. Proximal to the Alu insertion there is a small region where similarity between the X and Y chromosomes is reduced and which is no longer subject to recombination.

Filipski, J., J. Salinas, and F. Rodier. 1989. Chromosome localization-dependent compositional bias of point mutations in Alu repetitive sequences. J Mol Biol. 206(3):563-6.

The Alu repetitive sequence family originated from a common ancestor. Its members, apparently free from functional constraints, are interspersed throughout primate genomes. We have found that base substitutions occurring during the evolution of primates caused a decrease in the average G + C content of those members of the family that are located in an A + T-rich region of the genome. The family members that are located in a G + C-rich genomic region have not changed their, already high, G + C content. This suggests that the regional differences in G + C content, which are responsible for chromosomal banding, are caused by an accumulation of mutations that, although selectively neutral in the majority, show different compositional bias in different regions of the vertebrate chromosome.

Gonzalez, I. L., R. Petersen, and J. E. Sylvester. 1989. Independent insertion of Alu elements in the human ribosomal spacer and their concerted evolution. Mol Biol Evol. 6(4):413-23.

A 2,700-bp segment of human ribosomal DNA (rDNA) spacer upstream of the rRNA promoter contains a set of four Alu elements, two in the direction of rRNA transcription and two in the opposite orientation. We report and compare the sequences of these Alu elements found in three rDNA clones and seek to determine the origin of the cluster, either from a single insertion followed by duplications or from multiple simultaneous or independent insertions. The high (20%-27%) divergence among members of a set and the lack of similarity/complementarity of sequences flanking different members of the set demonstrate the independent insertion of each of the four Alu elements into A-rich sequences on the appropriate strand of the rDNA. We also demonstrate that the Alu sets found in different rDNA repeats are subject to concerted evolution, yielding divergences of only 0.4%-3% between Alu elements in equivalent positions. However, the pairs of adjacent similarly oriented Alu elements do not show reduced divergence, indicating that there is no recombination or gene conversion between similarly oriented but not equivalently positioned Alu elements. Finally, crossing-over must occur in the rDNA junction region between Alu element 3 and the nonribosomal sequences at the telomere end of the acrocentric chromosome, so that the Alu elements of the terminal rDNA repeats and the terminal repeats themselves evolve in concert with the rDNA repeats located internally in the tandem array.

Huang, L. S., M. E. Ripps, S. H. Korman, R. J. Deckelbaum, and J. L. Breslow. 1989. Hypobetalipoproteinemia due to an apolipoprotein B gene exon 21 deletion derived by Alu-Alu recombination. J Biol Chem. 264(19):11394-400.

We report the molecular defect in an individual with homozygous hypobetalipoproteinemia. A unique TaqI restriction fragment length polymorphism was found in the midportion of the apolipoprotein B (apoB) gene using the genomic probe, pB51. The probe, which identifies TaqI fragments of 8.4 and 2.8 kilobases (kb) in normal individuals, hybridized to a single 11-kb fragment in the proband. The parents of the proband showed all three TaqI fragments, implying that they are heterozygotes for the mutant apoB allele. In this family, the mutant allele cosegregated with low total cholesterol levels and formal linkage analysis gave a decimal logarithm of the ratio score of 3.3 at a recombination frequency of 0. The polymorphic TaqI site was localized to an EcoRI fragment of 4 kb in normal individuals. The corresponding fragment in the proband was 3.4 kb, suggesting a 0.6-kb deletion in the mutant allele. Both the normal 4-kb EcoRI fragment and the mutant 3.4- kb EcoRI fragment were cloned and sequenced. In the normal allele, the 4-kb EcoRI fragment extends from intron 20 to 23. Exon 21 is flanked by Alu sequences that are in the same orientation. The mutant allele had a 694-bp deletion in this region which included a small part of the Alu sequence in intron 20, the entire exon 21, and most of the Alu sequence in intron 21. The polymorphic TaqI site, which lies within the Alu sequence in intron 21, was absent in the proband as a result of the deletion. The deletion of exon 21 results in a frame shift mutation and the introduction of a stop codon. Translation of the encoded mRNA would yield a prematurely terminated protein. This mutant apoB protein would be 1085 amino acids long with the 73 carboxyl-terminal residues out of frame. We postulate that the deletion of exon 21 is the consequence of a crossover event between the Alu sequences in introns 20 and 21 resulting in nonreciprocal exchange between two chromosomes.

Jang, K. L., and D. S. Latchman. 1989. HSV infection induces increased transcription of Alu repeated sequences by RNA polymerase III. FEBS Lett. 258(2):255-8.

The Alu family of repeated sequences is transcribed by both RNA polymerase II and RNA polymerase III. In cells infected with HSV, transcription by polymerase III increases while transcription by polymerase II decreases. By using virus strains carrying mutations in the genes encoding individual regulatory proteins, we have shown that this effect is dependent upon the immediate-early protein ICP27 and occurs by a process distinct from those which regulate viral gene expression. This is the first example of increased transcription of endogenous cellular sequences by RNA polymerase III during infection with a DNA virus.

Kudo, S., and M. Fukuda. 1989. Structural organization of glycophorin A and B genes: glycophorin B gene evolved by homologous recombination at Alu repeat sequences. Proc Natl Acad Sci U S A. 86(12):4619-23.

Glycophorins A (GPA) and B (GPB) are two major sialoglycoproteins of the human erythrocyte membrane. Here we present a comparison of the genomic structures of GPA and GPB developed by analyzing DNA clones isolated from a K562 genomic library. Nucleotide sequences of exon- intron junctions and 5' and 3' flanking sequences revealed that the GPA and GPB genes consist of 7 and 5 exons, respectively, and both genes have greater than 95% identical sequence from the 5' flanking region to the region approximately 1 kilobase downstream from the exon encoding the transmembrane regions. In this homologous part of the genes, GPB lacks one exon due to a point mutation at the 5' splicing site of the third intron, which inactivates the 5' cleavage event of splicing and leads to ligation of the second to the fourth exon. Following these very homologous sequences, the genomic sequences for GPA and GPB diverge significantly and no homology can be detected in their 3' end sequences. The transition site from homologous to nonhomologous sequences can be localized within Alu repeat sequences. The analysis of the Alu sequences and their flanking direct repeat sequences suggest that an ancestral genomic structure has been maintained in the GPA gene, whereas the GPB gene has arisen from the acquisition of 3' sequences different from those of the GPA gene by homologous recombination at the Alu repeats during or after gene duplication.

Labuda, D., and G. Striker. 1989. Sequence conservation in Alu evolution. Nucleic Acids Res. 17(7):2477-91.

A statistical analysis of a set of genomic human Alu elements is based on a published alignment and a recent classification of these sequences. After separation of the Alu sequences into families, the consensus sequences of these families are determined, using the correct weighting of the unidirectional decay of CG-dinucleotides. For, the tenfold greater mutation rate at CG's requires separate consideration of an independent clock at every stage of analysis. The distributions of the substitutions with respect to the new consensus sequences, taking the CG and the non-CG-nucleotide positions separately, lie far closer to the expected distributions than the total diversity. Computer analysis of the folding of RNAs derived from these sequences indicates that RNA secondary structure is conserved among Alu families, suggesting its importance for Alu proliferation and/or function. The folding pattern, further substantiated by a number of compensatory mutations, includes secondary structure domains which are homologous to those observed in 7SL RNA and a defined region of interaction between the two Alu subunits. These results are consistent with a model in which a small number of conserved Alu master genes give rise via retroposition to the numerous copies of Alu pseudogenes, that then diversify by random substitution. The master genes appeared at different periods during evolution giving rise to different families of Alu sequences.

Lin, C. S., D. A. Goldthwait, and D. Samols. 1989. Identification of Alu transposition in human lung carcinoma cells: a correction [letter]. Cell. 59(1):9.

Miura, O., Y. Sugahara, Y. Nakamura, S. Hirosawa, and N. Aoki. 1989. Restriction fragment length polymorphism caused by a deletion involving Alu sequences within the human alpha 2-plasmin inhibitor gene. Biochemistry. 28(12):4934-8.

A restriction fragment length polymorphism within the human alpha 2- plasmin inhibitor gene has been detected by Southern blot hybridization using an alpha 2-plasmin inhibitor cDNA probe. This restriction fragment length polymorphism can be attributed to the presence of two alleles, A and B, that are distributed in Hardy-Weinberg equilibrium with frequencies of 73.5% and 2.65%, respectively, in 66 unrelated Caucasian individuals or with frequencies of 51.0% and 49.0%, respectively, in 50 unrelated Japanese individuals. The minor allele, B, is due to a deletion of about 720 base pairs in intron 8 of the alpha 2-plasmin inhibitor gene. Sequence analysis of the deletion junction in allele B and the corresponding regions of allele A demonstrated the presence of oppositely oriented Alu sequences at the 5' and 3' deletion boundaries. These data suggest that this restriction fragment length polymorphism was caused by intrastrand recombination between Alu sequences.

Nelson, D. L., S. A. Ledbetter, L. Corbo, M. F. Victoria, R. Ramirez-Solis, T. D. Webster, D. H. Ledbetter, and C. T. Caskey. 1989. Alu polymerase chain reaction: a method for rapid isolation of human- specific sequences from complex DNA sources. Proc Natl Acad Sci U S A. 86(17):6686-90.

Current efforts to map the human genome are focused on individual chromosomes or smaller regions and frequently rely on the use of somatic cell hybrids. We report the application of the polymerase chain reaction to direct amplification of human DNA from hybrid cells containing regions of the human genome in rodent cell backgrounds using primers directed to the human Alu repeat element. We demonstrate Alu- directed amplification of a fragment of the human HPRT gene from both hybrid cell and cloned DNA and identify through sequence analysis the Alu repeats involved in this amplification. We also demonstrate the application of this technique to identify the chromosomal locations of large fragments of the human X chromosome cloned in a yeast artificial chromosome and the general applicability of the method to the preparation of DNA probes from cloned human sequences. The technique allows rapid gene mapping and provides a simple method for the isolation and analysis of specific chromosomal regions.

Prasad, S. C., J. Boyle, and A. Dritschilo. 1989. Quantitation of strand breaks in human DNA using 32P-Alu hybridization: application to exponential and plateau-phase cells. Radiat Res. 117(3):538-46.

A sensitive quantitation of DNA (0.2 to 10 ng) can be achieved using a 32P-labeled Alu probe to hybridize human DNA spotted onto nylon membrane. This allows the determination of radiation-induced single- strand breaks without the use of [3H]thymidine prelabeling of cells in culture. The sensitivity of this technique in HeLa cells is comparable to results obtained using the alkaline unwinding technique. The method is applicable to cells in both exponential and plateau phases of growth.

Saffer, J. D., and S. J. Thurston. 1989. A negative regulatory element with properties similar to those of enhancers is contained within an Alu sequence. Mol Cell Biol. 9(2):355-64.

A negative regulatory element has been found within a member of the African green monkey Alu family of interspersed repeated sequences. This "reducer" element decreased transcription in both directions from a cellular simian virus 40-like bidirectional promoter independently of both orientation and position. The reducer was not promoter specific since it also decreased expression from the simian virus 40 early and human beta-globin promoters. In addition, the reducer decreased transcription from a polymerase III promoter. The reducer was contained in 38 base pairs of an Alu family member and interacted specifically with a monkey cell nuclear protein.

Tomilin, N. V., and V. M. Bozhkov. 1989. Human nuclear protein interacting with a conservative sequence motif of Alu-family DNA repeats. FEBS Lett. 251(1-2):79-83.

Human retrotransposons, Alu-family DNA repeats (AFRs), have variable nucleotide sequence but conservative short elements, which may have important functions, are also present. In our previous reports we have described human nuclear DNA-binding protein interacting with AFRs and evidence was presented that the protein recognizes sequence motif 5'- GGAGGC-3' which is conserved in the spacer of RNA polymerase III promoter of AFRs and in the SV40 T-antigen-dependent replication origin of AFRs. In this study it was found that double-stranded synthetic oligonucleotides containing indicated conservative sequences of AFRs actually have high-affinity binding site for HeLa nuclear protein. The data suggest that non-infected human cells contain nuclear DNA-binding protein which recognizes the conservative sequence motif of AFRs - GGAGGC.

Zuckerkandl, E., G. Latter, and J. Jurka. 1989. Maintenance of function without selection: Alu sequences as "cheap genes". J Mol Evol. 29(6):504-12.

Continued insertion into the genome of functional Alu sequences is expected to compensate for the functional eclipse of older sequences attributable to structural adulteration and can be presumed to establish a renewable store of functional sequences at a relatively elevated numerical level. This store of functional sequences could be maintained at almost no selective cost. A strategy of maintaining function in multiple sequence copies with selection limited to a very few master (source) sequences may be resorted to also by other types of DNA sequences that are generated repeatedly during evolution and that are spread over many sectors of the genome.

Britten, R. J., D. B. Stout, and E. H. Davidson. 1989. The current source of human Alu retroposons is a conserved gene shared with Old World monkey. Proc Natl Acad Sci U S A. 86(10):3718-22.

A significant fraction of human Alu repeated sequences are members of the precise, recently inserted class. A cloned member of this class has been used as a probe for interspecies hybridization and thermal stability determination. The probe was reassociated with human, mandrill, and spider monkey DNA under conditions such that only almost perfectly matching duplexes could form. Equally precise hybrids were formed with human and mandrill DNA (Old World monkey) but not with spider monkey DNA (New World). These measurements as well as reassociation kinetics show the presence in mandrill DNA of many precise class Alu sequences that are very similar or identical in quantity and sequence to those in human DNA. Human and mandrill are moderately distant species with a single-copy DNA divergence of about 6%. Nevertheless, their recently inserted Alu sequences arise by retroposition of transcripts of source genes with nearly identical sequences. Apparently a gene present in our common ancestor at the time of branching was inherited and highly conserved in sequence in both the lineage of Old World monkeys and the lineage of apes and man.

Britten, R. J., W. F. Baron, D. B. Stout, and E. H. Davidson. 1988. Sources and evolution of human Alu repeated sequences. Proc Natl Acad Sci U S A. 85(13):4770-4.

Alu repeated sequences arising in DNA of the human lineage during about the last 30 million years are closely similar to a modern consensus. Alu repeats arising at earlier times share correlated blocks of differences from the current consensus at diagnostic positions in the sequence. Using these 26 positions, we can recognize four subfamilies and the older ones are each successively closer to the 7SL sequence. It appears that there has existed a series of conserved genes that are the primary sources of the Alu repeat family, presumably through retroposition. These genes have probably replaced each other in overlapping relays during the evolution of primates.

Chuang, L. M., B. J. Lin, S. C. Lee, T. Y. Tai, and D. S. Chen. 1988. Induction of an Alu-sequence containing transcript by insulin in human hepatoma cells. Biochem Biophys Res Commun. 156(3):1287-92.

A cDNA clone, designated AF19-1, was isolated from a cDNA library derived from insulin-stimulated hepatoma cells. The nucleotide sequences of AF19-1 showed 83% homology to Alu consensus sequence. It contained a full-length 300-bp Alu family sequence followed in direct tandem by a partial sequence of Alu left monomer. Primer extension analysis confirmed that this Alu transcript was induced even in short- term insulin stimulation. The increase in Alu-transcripts in the early phase of insulin stimulation in hepatoma cells suggests that the Alu sequences may play some important regulatory roles in gene expression.

Chung, L. P., S. Keshav, and S. Gordon. 1988. Cloning the human lysozyme cDNA: inverted Alu repeat in the mRNA and in situ hybridization for macrophages and Paneth cells. Proc Natl Acad Sci U S A. 85(17):6227-31.

Lysozyme is a major secretory product of human and rodent macrophages and a useful marker for myelomonocytic cells. Based on the known human lysozyme amino acid sequence, oligonucleotides were synthesized and used as probes to screen a phorbol 12-myristate 13-acetate-treated U937 cDNA library. A full-length human lysozyme cDNA clone, pHL-2, was obtained and characterized. Sequence analysis shows that human lysozyme, like chicken lysozyme, has an 18-amino-acid-long signal peptide, but unlike the chicken lysozyme cDNA, the human lysozyme cDNA has a greater than 1-kilobase-long 3' nontranslated sequence. Interestingly, within this 3' region, an inverted repeat of the Alu family of repetitive sequences was discovered. In RNA blot analyses, DNA probes prepared from pHL-2 can be used to detect lysozyme mRNA not only from human but also from mouse and rat. Moreover, by in situ hybridization, complementary RNA transcripts have been used as probes to detect lysozyme mRNA in mouse macrophages and Paneth cells. This human lysozyme cDNA clone is therefore likely to be a useful molecular probe for studying macrophage distribution and gene expression.

Deininger, P. L., and V. K. Slagel. 1988. Recently amplified Alu family members share a common parental Alu sequence. Mol Cell Biol. 8(10):4566-9.

Three of the most recently inserted primate Alu family members are exceptionally closely related. Therefore, one, or a few, Alu family members are dominating the amplification process and the vast majority are not actively involved in retroposition. Although individual Alu family members are not under any apparent evolutionary constraint, the sequences of these active members are being moderately conserved.

Filatov, L. V., S. E. Mamayeva, and N. V. Tomilin. 1988. 'Conservative' and 'variable' clusters of Alu-family DNA repeats in human chromosomes. Mol Biol Rep. 13(2):79-84.

The distribution of Alu-family DNA repeats (AFRs) in chromosomes of phytohaemagglutinin-stimulated peripheral blood lymphocytes of four normal donors and non-stimulated bone marrow cells of four patients with acute leukemia (ALL and ANLL) was studied by in situ hybridization using DNA of recombinant phage lambda containing multiple inserts of AFR as a probe. Over some chromosome bands (14cen, 16p13, 16cen) from normal donors and from leukemic patients clusters of silver grains were detected. Over other three bands (3q26, 8p11-p12 and 14q24) the clusters were found only in chromosomes from the four acute leukemia patients, and were absent from chromosomes of healthy donors. The results suggest non-random long-range distribution of AFRs in human chromosomes, and somatic variations in the distribution of the repeats.

Jurka, J., and T. Smith. 1988. A fundamental division in the Alu family of repeated sequences. Proc Natl Acad Sci U S A. 85(13):4775-8.

The Alu family of repeated sequences from the human genome contains two distinct subfamilies. This division is based on different base preferences in a number of diagnostic sequence positions. One subfamily of the sequences, referred to as the Alu-J subfamily, is very similar to 7SL DNA in these positions. The other subfamily, Alu-S, can be divided further into well-defined branches of sequences. These findings revise the previous picture of the Alu family and expose their complex evolutionary dynamics. They reveal sequence variations of potential importance for the proliferation of Alu repeats and relate them to their structural features. In addition, they open the possibility of using different types of Alu sequences as natural markers for studying genetic rearrangements in the genome.

Jurka, J., T. F. Smith, and D. Labuda. 1988. Small cytoplasmic Ro RNA pseudogene and an Alu repeat in the human alpha-1 globin gene. Nucleic Acids Res. 16(2):766.

Korenberg, J. R., and M. C. Rykowski. 1988. Human genome organization: Alu, lines, and the molecular structure of metaphase chromosome bands. Cell. 53(3):391-400.

Combining high resolution in situ hybridization with quantitative solid state imaging, we show that human metaphase chromosome Giemsa/Quinacrine and Reverse bands are each characterized by distinct families of interspersed repeated sequences: the SINES, Alu family dominates in Reverse bands, and the LINES, L1 family dominates in Giemsa/Quinacrine positive bands. Alu is 56% guanine plus cytosine, and L1 is 58% adenine plus thymine, and each may comprise 13%-18% of the total DNA in a chromosome band. Therefore, the distribution of these sequences alone may account for a large part of human chromosome banding seen with fluorescent dyes. With the exception of some telomeric regions, and the chromosomal regions of simple sequence DNA, Alu and L1 are precisely inversely distributed, suggesting an inverse functional relationship. This finding links genome organization with chromosome structure and function.

Lin, C. S., D. A. Goldthwait, and D. Samols. 1988. Identification of Alu transposition in human lung carcinoma cells. Cell. 54(2):153-9.

We have demonstrated genetic transposition in human cells. An experimental system was established in which the Ecogpt (gpt) gene was employed as a target for inactivation. The human lung carcinoma cell line A549 containing this target was fused to UV-irradiated A549 cells that did not contain the target. From the fusion products, sublines carrying an inactivated gpt gene were analyzed. UV irradiation increased the frequency of inactivated gpt genes in the fusion cells by 100-fold. One subline was found to contain a complete Alu sequence in the coding region of the gpt gene. The inserted element differed from the Blur8 sequence by only 7 out of the 270 nucleotides. The insertion of this Alu element created a 5 bp insertion site duplication.

Markert, M. L., J. J. Hutton, D. A. Wiginton, J. C. States, and R. E. Kaufman. 1988. Adenosine deaminase (ADA) deficiency due to deletion of the ADA gene promoter and first exon by homologous recombination between two Alu elements. J Clin Invest. 81(5):1323-7.

In 15-20% of children with severe combined immunodeficiency (SCID), the underlying defect is adenosine deaminase (ADA) deficiency. The goal of this study was to determine the precise molecular defect in a patient with ADA-deficient SCID whom we previously have shown to have a total absence of ADA mRNA and a structural alteration of the ADA gene. By detailed Southern analysis, we now have determined that the structural alteration is a deletion of approximately 3.3 kb, which included exon 1 and the promoter region of the ADA gene. DNA sequence analysis demonstrates that the deletion created a novel, complete Alu repeat by homologous recombination between two existing Alu repeats that flanked the deletion. The 26-bp recombination joint in the Alu sequence includes the 10-bp "B" sequence homologous to the RNA polymerase III promoter. This is the first example of homologous recombination involving the B sequence in Alu repeats. Similar recombination events have been identified involving Alu repeats in which the recombination joint was located between the A and B sequences of the polymerase III split promoter. The nonrandom location of these events suggests that these segments may be hot spots for recombination.

Podgornaya, O. I., L. M. Perelygina, and N. V. Tomilin. 1988. Multi-site binding of human nuclear protein to the Alu-family repeated DNA. FEBS Lett. 232(1):99-102.

Nuclear protein which selectively binds to the Alu-family DNA repeat (AFR, Blur8) is partially purified from human HeLa cells using a gel retention assay. At low protein concentrations only a single complex of the protein with AFR is formed (CII). Increasing protein concentrations lead to the gradual disappearance of CII, being replaced by complexes with higher (CI) and lower (CIII, CIV) electrophoretic mobilities. Differential binding of AFR restriction subfragments indicates that multiple protein-binding sites are present within AFR. We discuss two models explaining the anomalous electrophoretic mobility of CII by DNA bending or looping upon cooperative multi-site binding of the protein to AFR.

Quentin, Y. 1988. The Alu family developed through successive waves of fixation closely connected with primate lineage history. J Mol Evol. 27(3):194-202.

A new method of analyzing phylogenetic relations among members of the sequence family is presented and applied to human Alu sequences upon which work has been published. This method, based upon a correspondence analysis, works with large samples and yields easily interpretable graphical representations. Results obtained argue in favor of a new evolutionary scheme for Alu sequences, implying successive waves of amplification/fixation closely connected to primate lineage history.

Schedlich, L. J., and B. J. Morris. 1988. Three Alu repeated sequences associated with a human glandular kallikrein gene. Clin Exp Pharmacol Physiol. 15(4):339-44.

1. Recently the complete primary structure of a human glandular kallikrein gene, hGK-1, was reported. The present paper presents further structural information. 2. Associated with the gene were three Alu repeated sequences; one in the second intron and two approximately 0.4 kb and 1.2 kb upstream. 3. The 5' non-coding and 5' flanking DNA was highly homologous to that in the mouse genes. 4. Different polyadenylation signals are used in different human kallikrein genes.

Trus, M., K. Lord, D. Liebermann, and B. Hoffman-Liebermann. 1988. TU-Alu: variant Alu elements with homology to TU transposons. Nucleic Acids Res. 16(23):11385.

Assouline, Z., D. M. Kerbiriou-Nabias, G. Pietu, N. Thomas, B. R. Bahnak, and D. Meyer. 1988. The human gene for von Willebrand factor. Identification of repetitive Alu sequences 5' to the transcription initiation site. Biochem Biophys Res Commun. 153(3):1159-66.

The region at the 5' end of von Willebrand factor gene was cloned by screening genomic libraries with a partial von Willebrand factor cDNA probe and oligonucleotides complementary to areas of von Willebrand factor mRNA at the extreme 5' end of the untranslated region. The sequence 2158 bp upstream of the transcription initiation site, the first exon and first exon-intron junction is reported. The first exon includes the entire 5' untranslated sequence (250 bp) and the translation initiation codon starts the second exon, suggesting an unusual control mechanism for the cell specific expression of von Willebrand factor. An AT-rich region resembling a TATA box is found 32 bp upstream of the transcription initiation site. At -1030 and -1806 nucleotides 5' of the TATA box are two repetitive Alu sequences of approximately 300 bp. Recombinant events at these Alu sequences could result in some clinical forms of von Willebrand disease involving transcriptional defects.

Filatov, L. V., S. E. Mamayeva, and N. V. Tomilin. 1987. Non-random distribution of Alu-family repeats in human chromosomes. Mol Biol Rep. 12(2):117-22.

A phage lambda recombinant clone containing at least 8 Alu-family repeats (AFRs) has been isolated from a human genomic library, and DNA from the phage was used as a probe for in situ hybridization on G- banded human metaphase chromosomes of healthy donors and leukemic patients. Some chromosome bands show prominent clusters of silver grains in all individuals examined: 1p34, 1q23, 2q21-22, 10p14, 11p14, 10q21 and 11q14. The data suggest non-random distribution of AFRs in the human genome.

Horsthemke, B., U. Beisiegel, A. Dunning, J. R. Havinga, R. Williamson, and S. Humphries. 1987. Unequal crossing-over between two alu-repetitive DNA sequences in the low-density-lipoprotein-receptor gene. A possible mechanism for the defect in a patient with familial hypercholesterolaemia. Eur J Biochem. 164(1):77-81.

We have previously identified a patient with familial hypercholesterolaemia (FH), where the defect appears to be caused by a deletion in the 3' region of the low-density lipoprotein (LDL)-receptor gene. We have now isolated the LDL-receptor gene from the patient and have studied the defect at the DNA level. Restriction mapping and sequence analysis demonstrate that a 4-kb DNA deletion has occurred between two alu-repetitive sequences that are in the same orientation, one in intron 12 and the other in intron 14. This deletion eliminates exons 13 and 14, and changes the reading frame of the resulting spliced mRNA such that a stop codon is created in the following exon. Immuno- and ligand-blot analysis using cultured fibroblasts from this patient revealed the normal gene product, but failed to detect any smaller receptor protein. This implies that the truncated receptor protein that is synthesised is rapidly degraded. We suggest that in this patient the deletion is caused by an unequal crossing-over event that occurred between two homologous chromosomes at meiosis.

Hyrien, O., M. Debatisse, G. Buttin, and B. R. de Saint Vincent. 1987. A hotspot for novel amplification joints in a mosaic of Alu-like repeats and palindromic A + T-rich DNA. Embo J. 6(8):2401-8.

We have identified, in the amplified domain of adenylate deaminase (AMPD) overproducing Chinese hamster fibroblasts, a 2.6 kb recombinogenic DNA region which is frequently involved in amplification- associated rearrangements. The nucleotide sequence reveals a mosaic organization of four Alu-equivalent repeats of the B1 and B2 families and eight long A + T-rich DNA segments. Part of this region is enriched with long imperfect palindromes. The center of one palindrome contains a putative topoisomerase I cleavage site and this site defines the position of a novel junction which was formed by illegitimate recombination with anther A + T-rich DNA sequence located far apart on the amplified DNA. These findings and their significance are discussed in the context of related data from other systems and in the light of current models for eukaryotic DNA recombination, replication and organization.

Indik, Z., K. Yoon, S. D. Morrow, G. Cicila, J. Rosenbloom, and N. Ornstein-Goldstein. 1987. Structure of the 3' region of the human elastin gene: great abundance of Alu repetitive sequences and few coding sequences. Connect Tissue Res. 16(3):197-211.

Two overlapping clones encompassing 8.5 kb of the human elastin gene were isolated from two genomic libraries constructed by partial digestion with either HaeIII/AluI or Sau3A and contained in lambda Charon 4A or EMBL3, respectively. The 6 kb of DNA comprising the most 3' portion of the gene were sequenced demonstrating an extremely low coding ratio since only three exons containing a total of 134 translated nucleotides were identified. Two exons totaling 78 bp of translated sequences which were previously found in the bovine gene were absent in the human gene. The 3' most exon encoded the unusual amino acid sequence, GGACLGKACGRKRK. The human gene was terminated by 1.2 kb of untranslated sequence which contained two polyadenylation attachment signals. The remainder of the 6 kb was composed of intervening sequences which were abundantly rich in Alu family repetitive sequences found in both orientations. This first report of the characterization of the human elastin gene suggests that significant variation in the gene may exist between species and raises the possibility of consequential polymorphism, mediated by recombination between Alu sequences, in the human population.

Jaiswal, A. K., D. W. Nebert, O. W. McBride, and F. J. Gonzalez. 1987. Human P(3)450: cDNA and complete protein sequence, repetitive Alu sequences in the 3' nontranslated region, and localization of gene to chromosome 15. J Exp Pathol. 3(1):1-17.

P(1)450 and P(3)450 are the two members of the dioxin-inducible P450 gene family, one of at least eight families in the entire P450 gene superfamily. The human P(1)450 gene has been previously sequenced. In this report the human liver P(3)450 protein is shown to migrate as a 54- kDa band on NaDodSO4-polyacrylamide gel electrophoresis. The human P(3)450 cDNA (3,064 bp) and complete P(3)450 protein (515 residues; Mr = 58,294) were determined. The human P(3)450 mRNA (3.3 kb) has an unusually long 3' nontranslated region (1,509 bp) primarily due to the inclusion of four copies of Alu repetitive sequences. Comparison of human P(3)450 cDNA with human P(1)450 cDNA and mouse (or rat) P(3)450 cDNA with mouse (or rat) P(1)450 cDNA suggests that an intra-exonic gene conversion event (in the region between 100 and 400 nucleotides from the 5' end of the translated region) most likely occurred between 20 and 80 million years ago. Analysis of 32 human X mouse and 23 human X hamster somatic cell hybrids confirm unequivocally that both P(3)450 and P(1)450 reside on human chromosome 15.

Kariya, Y., K. Kato, Y. Hayashizaki, S. Himeno, S. Tarui, and K. Matsubara. 1987. Revision of consensus sequence of human Alu repeats--a review. Gene. 53(1):1-10.

Nucleotide sequences of 50 human Alu repeats and their flanking regions are presented together with the consensus sequence based on the literature and our findings. The results indicate the need for some revisions of the Alu consensus sequence published by Deininger et al. (1981). Most nucleotide substitutions among the Alu members are transitions, rather than transversions. The Alu sequence seems to consist of 'conserved' regions and 'variable' regions. The conserved regions consist of a 25-bp region between nt positions 23 and 47 and a 16-bp region between nt positions 245 and 260. The 16-bp region corresponds to the region of 7SL RNA that is claimed to fold and become paired with the internal promoter sequence. Two A-rich regions, one located at the right end of the first monomer and the other at the right end of the second monomer, are variable. No defined property was found with direct repeats flanking the Alu repeats.

Lehrman, M. A., J. L. Goldstein, D. W. Russell, and M. S. Brown. 1987. Duplication of seven exons in LDL receptor gene caused by Alu-Alu recombination in a subject with familial hypercholesterolemia. Cell. 48(5):827-35.

A defective LDL receptor gene in a child with familial hypercholesterolemia produces a receptor precursor that is 50,000 daltons larger than normal (apparent Mr 170,000 vs. 120,000). The elongated protein resulted from a 14 kilobase duplication that encompasses exons 2 through 8. The duplication arose from an unequal crossing-over between homologous repetitive elements (Alu sequences) in intron 1 and intron 8. The mutant receptor has 18 contiguous cysteine- rich repeat sequences instead of the normal nine. Seven of these duplicated repeats are derived from the ligand-binding domain, and two repeats are part of the epidermal growth factor precursor homology region. The elongated receptor undergoes normal carbohydrate processing, its apparent molecular weight increases to 210,000, and the receptor reaches the cell surface where it binds reduced amounts of LDL but undergoes efficient internalization and recycling. The current findings support an evolutionary model in which homologous recombination between repetitive elements in introns leads to exon duplication during evolution of proteins.

Lehrman, M. A., D. W. Russell, J. L. Goldstein, and M. S. Brown. 1987. Alu-Alu recombination deletes splice acceptor sites and produces secreted low density lipoprotein receptor in a subject with familial hypercholesterolemia. J Biol Chem. 262(7):3354-61.

A Japanese subject with homozygous familial hypercholesterolemia was found to have a 7.8-kilobase deletion in the gene for the low density lipoprotein receptor. The deletion joins intron 15 to the middle of exon 18, which encodes the 3' untranslated region, thereby removing all 3' splice acceptor sites distal to intron 15. By S1 nuclease mapping, we demonstrated that the 5' splice donor site of intron 15 is no longer used. Instead a continuous transcript is produced in which exon 15 is followed by the remaining segments of intron 15 and exon 18. The translational reading frame of exon 15 continues for 165 nucleotides into intron 15 before a termination codon is reached. This mRNA should produce a truncated receptor that lacks the normal membrane-spanning region and cytoplasmic domain and that has 55 novel amino acids at its COOH terminus. A cDNA expression vector containing this sequence produced a receptor that behaved similarly to the truncated protein produced by the Japanese patient, i.e. greater than 90% of the receptor was secreted from the cell, and the receptors remaining on the surface showed defective internalization. The deletion in this subject resulted from a recombination between two repetitive sequences of the Alu family, one in intron 15 and the other in exon 18. To date, Alu sequences have been observed at the deletion joints of all four gross deletions in the low density lipoprotein receptor gene that have been characterized. Within these Alu sequences, six out of the seven breakpoints have occurred in the left arm. These data suggest that recombination between Alu sequences may be a frequent cause of deletions in the human genome.

Limborska, S. A., S. A. Korneev, N. E. Maleeva, P. A. Slominsky, A. G. Jincharadze, P. L. Ivanov, and A. P. Ryskov. 1987. Cloning of Alu-containing cDNAs from human fibroblasts and identification of small Alu+ poly(A)+ RNAs in a variety of human normal and tumor cells. FEBS Lett. 212(2):208-12.

Two clones have been selected from a human fibroblast cDNA bank. By DNA sequencing the clones were shown to contain Alu elements located near the ends of the cDNA inserts. DNA of the clones was used for Northern blot hybridization analysis of a number of poly(A)-containing RNAs from normal human tissues (brain, stomach, uterus, spleen, fibroblasts) and tumors (neurinoma, glioma, neuroblastoma, liposarcoma, adrenal cortex adenocarcinoma). All RNA samples reveal a heterodisperse distribution of Alu transcripts with discrete bands in the region of 7-12 S RNA. The majority of these small poly(A)+ Alu+ RNAs contain Alu sequences only in one (canonical) orientation with functional signals including the split promoter for RNA polymerase III.

Myerowitz, R., and N. D. Hogikyan. 1987. A deletion involving Alu sequences in the beta-hexosaminidase alpha- chain gene of French Canadians with Tay-Sachs disease. J Biol Chem. 262(32):15396-9.

French Canadians living in eastern Quebec are carriers of a severe type of Tay-Sachs disease, known as the classic form, 10 times more often than the general population. The alpha-chain of beta-hexosaminidase A, a lysosomal enzyme composed of two chains (alpha, beta), bears the mutation in this inherited disorder. We previously reported that the 5' end of the alpha-chain gene was deleted in two such patients (Myerowitz, R., and Hogikyan, N.D. (1986) Science, 232, 1646-1648). The present study reports the size, precise location, and environment of the deletion. A clone encompassing the deletion was isolated from a genomic library constructed in lambda EMBL3 with DNA from a patient's fibroblasts. Comparison of the restriction maps of the clone with that of the normal gene (Proia, R.L., and Soravia, E. (1987) J. Biol. Chem. 262, 5677-5681) showed that the deletion was 7.6 kilobases long and included part of intron 1, all of exon 1 and extended 2000 base pairs upstream past the putative promotor region of the alpha-chain gene. These data are consistent with the inability to detect mRNA and immunoprecipitable alpha-chain protein in this mutant. Sequence analysis of the deletion junction in the mutant and corresponding regions of the normal gene demonstrated the presence of similarly oriented Alu sequences at the 5' and 3' deletion boundaries. The data are in accord with the possibility that the deletion may have arisen during homologous recombination from unequal crossing over between Alu sequences.

Perelygina, L. M., N. V. Tomilin, and O. I. Podgornaya. 1987. Alu-family repeat binding protein from HeLa cells which interacts with regulatory region of SV40 virus genome. Mol Biol Rep. 12(2):111-6.

Using a gel retardation assay the protein which binds selectively to the Alu-family repeat (AFR) has been identified and partially purified from HeLa cell nuclear extract. The protein (AFR-binding protein, ABP) forms multiple discrete complexes with AFR even in the presence of 200 to 2000-fold excess of non-specific (E. coli) DNA. The most stable complex has a relative mobility in 4% polyacrylamide gel (as compared to the free Alu-fragment) of 0.54. Heterogeneity of protein-DNA bands seen in the polyacrylamide gel suggests that ABP is able to form multimeric complexes with AFR. Competition experiments show that ABP does not interact with the RNA polymerase III promoter and with the TGGCA-sequence, but a high affinity binding site for ABP was found within a 660 bp restriction fragment containing the SV40 virus promoter and replication origin.

Rouyer, F., M. C. Simmler, D. C. Page, and J. Weissenbach. 1987. A sex chromosome rearrangement in a human XX male caused by Alu-Alu recombination. Cell. 51(3):417-25.

Human XX maleness is often due to the presence of Y-specific DNA, resulting from abnormal interchange of terminal parts of the short arms of the X and Y chromosomes. In an XX male, a rearrangement is observed at locus DXYS5, the most proximal Yp locus detected in this patient. Cloning and analysis of the rearranged DNA fragment revealed pseudoautosomal sequences located beyond the breakpoint. We propose that this XX male arose by abnormal crossing over between DXYS5 on the Y chromosome and a pseudoautosomal locus on the X chromosome during paternal meiosis. Sequence analysis of the junction shows that homologous recombination occurred between two Alu sequences from these otherwise nonhomologous regions. The site of recombination is localized to the putative transcription promoter region of the Alu sequences.

Rubinstein, W. S., and J. W. Gordon. 1987. Restriction enzyme evidence for Alu sequence-mediated dispersion of microinjected genes in transgenic mice. Dev Genet. 8(4):233-47.

A human bacteriophage clone containing adult beta-globin genes with four Alu sequences was microinjected to produce transgenic mice. Southern blot analysis on the spleen of a transgenic mouse revealed an unusual hybridization pattern that suggested extensive dispersion of human DNA throughout the mouse genome. This pattern was reproducible using several restriction enzymes, including a noncutting enzyme. The hybridization pattern was not observed in other tissues, and sequences were not detected in progeny using the bacteriophage probe. However, hybridization of spleen DNA of offspring against a human Alu probe revealed genetic transmission of human Alu sequences. The results suggest dispersion of microinjected Alu sequences throughout the genome.

Ruffner, D. E., C. N. Sprung, P. P. Minghetti, P. E. Gibbs, and A. Dugaiczyk. 1987. Invasion of the human albumin-alpha-fetoprotein gene family by Alu, Kpn, and two novel repetitive DNA elements. Mol Biol Evol. 4(1):1-9.

The human albumin-alpha-fetoprotein genomic domain contains 13 repetitive DNA elements randomly distributed throughout the symmetrical structures of these genes. These repeated sequences are located at different sites within the two genes. The human albumin gene contains five Alu elements within four of its 14 intervening sequences. Two of these repeats are located in intron 2, and the remaining three are located in introns 7, 8, and 11. The human alpha-fetoprotein gene contains three of these Alu elements, one in intron 4 and the remaining two in the 3'-untranslated region. In addition, the human alpha- fetoprotein gene contains a Kpn repeat and two classes of novel repeats that are absent from the human albumin gene. Six of the Alu elements within the two genes are bound by short direct repeats that harbor five base substitutions in 120 possible positions (60 bp times 2 termini). The absence of Alu repeats from analogous positions in rodents indicates that these repeats invaded the albumin-alpha-fetoprotein domain less than 85 Myr ago (the time of mammalian radiation). Furthermore, considering the conservation of terminal repeats flanking the Alu sequences of the albumin-alpha-fetoprotein domain (0.042 changes per site), we submit that the average time of Alu insertion into this gene family could have been as recently as 15-30 Myr ago.

Slagel, V., E. Flemington, V. Traina-Dorge, H. Bradshaw, and P. Deininger. 1987. Clustering and subfamily relationships of the Alu family in the human genome. Mol Biol Evol. 4(1):19-29.

Thirteen and 10 sequences of the Alu family of repeated DNA elements found within the human thymidine kinase and beta-tubulin genes, respectively, were compared. These genes have approximately five times the expected density of Alu family members. The consensus sequence that could be drawn from these 23 Alu family members would differ slightly from others drawn from random Alu family sequences but only at very heterogeneous positions. The different Alu family members do show different pairwise percentage identities, with approximately 15% (7 of 48 Alu family members analyzed) of them clearly representing a separate subfamily of sequences. This analysis also confirms the species- specific differences between human and the prosimian Galago crassicaudatus Alu family members. These data are consistent with both the origin of these sequences in primates less than 65-70 Myr ago and amplification since that time to their present 500,000 copies. The data do not show any special relationships among densely clustered Alu family members.

Trabuchet, G., Y. Chebloune, P. Savatier, J. Lachuer, C. Faure, G. Verdier, and V. M. Nigon. 1987. Recent insertion of an Alu sequence in the beta-globin gene cluster of the gorilla. J Mol Evol. 25(4):288-91.

We present the nucleotide sequence of a new Alu family member that lies between the delta- and beta-globin genes in gorilla DNA. The sequence exhibits 91% similarity with a consensus sequence of the Alu family. It is flanked by a perfect repetition of a 16-nucleotide target sequence and terminates with 24 adenylic residues. As this sequence is absent at this locus in other primate DNAs, its insertion occurred less than 8 million years ago, thus supporting the idea that Alu sequences are still mobile elements in the hominoid genome.

Watson, J. B., and J. G. Sutcliffe. 1987. Primate brain-specific cytoplasmic transcript of the Alu repeat family. Mol Cell Biol. 7(9):3324-7.

A 200-nucleotide RNA homologous to the left monomer of Alu elements was expressed in monkey and human brain and in cell lines but not in nonneural monkey tissues. Similar brain-specific transcription of identifier sequences was observed in rats. Thus, expression of selected repetitive DNA families is a conserved process in mammalian brain.

Willard, C., H. T. Nguyen, and C. W. Schmid. 1987. Existence of at least three distinct Alu subfamilies. J Mol Evol. 26(3):180-6.

Computer-assisted sequence analysis of human Alu family members reveals that Alu repeats belong to one of at least three subfamilies. The insertion of human Alu repeats can be represented by three episodic bursts, each of which was founded by a distinct master sequence.

Andrews, P. G., and R. Kole. 1987. Alu RNA transcribed in vitro binds the 68-kDa subunit of the signal recognition particle. J Biol Chem. 262(6):2908-12.

Antibodies directed against the 68-kDa subunit of signal recognition particle (SRP) precipitate an Alu RNA X protein complex formed during in vitro transcription of a plasmid containing an Alu family sequence. The same Alu RNA X protein complex is precipitated by anti-Alu sera from certain patients with systemic lupus erythematosus and related autoimmune diseases (Kole, R., Fresco, L. D., Keene, J. D., Cohen, P. L., Eisenberg, R. A., and Andrews, P. G. (1985) J. Biol. Chem. 260, 11781-11786). Similarly to anti-SRP antibodies human, anti-Alu sera precipitate SRP from HeLa cell extract and detect a 68-kDa SRP subunit on immunoblots. These results indicate that the Alu antigen and the 68- kDa SRP subunit are the same polypeptide.

Bains, W. 1986. The multiple origins of human Alu sequences. J Mol Evol. 23(3):189-99.

I have analyzed a collection of published human Alu sequences. The compiled sequences show several unexpected features, including a uniform pattern of divergence from their consensus sequence, a mutual divergence that is not correlated with their age, and common features in the genomic DNA flanking the 5' ends of the elements. I suggest that the Alu family of sequences derives from a large pool of precursors and not from a single precursor similar to the family consensus sequence, and that new elements integrate into the genome selectively at oligo-A- rich sites.

Johnson, E. M., and W. R. Jelinek. 1986. Replication of a plasmid bearing a human Alu-family repeat in monkey COS-7 cells. Proc Natl Acad Sci U S A. 83(13):4660-4.

Monkey COS-7 cells were transformed with BLUR8 DNA, a pBR322 plasmid containing a human Alu-family sequence at the BamHI site. Within 24 hr of transformation 2-5% of the BLUR8 molecules recovered resisted cleavage by Dpn I, indicating they had replicated. Electron microscopy revealed appropriately sized circular molecules with replication bubbles whose centers were mapped to the Alu insert. A 16-base-pair deletion within the Alu sequence prevented replication. The results indicate that certain Alu sequences can serve as origins of replication in COS-7 cells.

Koop, B. F., M. M. Miyamoto, J. E. Embury, M. Goodman, J. Czelusniak, and J. L. Slightom. 1986. Nucleotide sequence and evolution of the orangutan epsilon globin gene region and surrounding Alu repeats. J Mol Evol. 24(1-2):94-102.

We have mapped and sequenced the epsilon globin gene and seven surrounding Alu repeat sequences in the orangutan beta globin gene cluster and have compared these and other orangutan sequences to orthologously related human sequences. Noncoding flanking and intron sequences, synonymous sites of alpha, gamma, and epsilon globin coding regions, and Alu sequences in human and orangutan diverge by 3.2%, 2.7%, and 3.7%, respectively. These values compare to 3.6% from DNA hybridizations and 3.4% from the psi eta globin gene region. If as suggested by fossil evidence and "molecular clock" calculations, human and orangutan lineages diverged about 10-15 MYA, the rate of noncoding DNA evolution in the two species is 1.0-1.5 X 10(-9) substitutions per site per year. We found no evidence for either the addition or deletion of Alu sequences from the beta globin gene cluster nor is there any evidence for recent concerted evolution among the Alu sequences examined. Both phylogenetic and phenetic distance analyses suggest that Alu sequences within the alpha and beta globin gene clusters arose close to the time of simian and prosimian primate divergence (about 50- 60 MYA). We conclude that Alu sequences have been evolving at the rate typical of noncoding DNA for the majority of primate history.

Lehrman, M. A., D. W. Russell, J. L. Goldstein, and M. S. Brown. 1986. Exon-Alu recombination deletes 5 kilobases from the low density lipoprotein receptor gene, producing a null phenotype in familial hypercholesterolemia. Proc Natl Acad Sci U S A. 83(11):3679-83.

Among patients with familial hypercholesterolemia, half of the mutant alleles at the low density lipoprotein (LDL) receptor locus produce no immunologically detectable protein. To determine the molecular basis for one such null allele, we have cloned an abnormally short restriction fragment from the genomic DNA of one patient. The DNA sequence revealed a 5-kilobase deletion that joins a coding sequence in exon 13 to an Alu repetitive element in intron 15. The deletion joint is flanked by two inverted repeats that could potentially form a double stem-loop structure that might have predisposed to this deletion. A similar double stem-loop structure can be drawn for a previously described deletion in the LDL receptor gene and for a deletion in the beta-globin gene cluster. We speculate that such double stem-loop structures might contribute to the formation of large deletions in the human genome.

Paulson, K. E., and C. W. Schmid. 1986. Transcriptional inactivity of Alu repeats in HeLa cells. Nucleic Acids Res. 14(15):6145-58.

The in vivo transcription of human Alu family members has been investigated by a sensitive primer extension method. The selected primers represent various regions of the Alu family consensus sequence, thus assaying the transcriptional activity of the entire family rather than the activity of an individual member sequence. Using this method, a very small number of RNA molecules per HeLa cell is found to have a distribution of 5' ends centered on the in vitro Alu transcription start site. The distribution of these 5' ends suggests that they are more likely the result of hnRNA degradation rather than transcription start sites. Therefore, despite their great numerical abundance, Alu family members are transcriptionally silent in HeLa cells.

Perez-Stable, C., and C. K. Shen. 1986. Competitive and cooperative functioning of the anterior and posterior promoter elements of an Alu family repeat. Mol Cell Biol. 6(6):2041-52.

Similar to tRNA genes and the VAI gene, the Alu family repeats are transcribed by RNA polymerase III and contain a split intragenic promoter. Results of our previous studies have shown that when the anterior, box A-containing promoter element (5'-Pu-Pu-Py-N-N-Pu-Pu-Py-G- G-3' in which Pu is any purine, Py is any pyrimidine, and N is any nucleotide) of a human Alu family repeat is deleted, the remaining box B-containing promoter element (5'-G-A/T-T-C-Pu-A-N-N-C-3') is still capable of directing weak transcriptional initiation at approximately 70 base pairs (bp) upstream from the box B sequence. This is different from the tRNA genes in which the box A-containing promoter element plays the major role in the positioning of the transcriptional initiation site(s). To account for this difference, we first carried out competition experiments in which we show that the posterior element of the Alu repeat competes with the VAI gene effectively for the transcription factor C in HeLa cell extracts. We then constructed a series of contraction and expansion mutants of the Alu repeat promoter in which the spacing between boxes A and B was systematically varied by molecular cloning. In vitro transcription of these clones in HeLa cell extracts was analyzed by RNA gel electrophoresis and primer extension mapping. We show that when the box A and box B promoter sequences are separated by 47 to 298 bp, the transcriptional initiation sites remain 4 to 5 bp upstream from box A. However, this positioning function by the box A-containing promoter element was lost when the spacing was shortened to only 26 bp or increased to longer than 600 bp. Instead, transcriptional initiation occurred approximately 70 bp upstream from box B, similar to that in the clones containing only the box B promoter element. All the mutant clones were transcribed less efficiently than was the wild type. An increase in the distance between boxes A and B also activated a second box A-like element within the Alu family repeat. We compare these results with the results of tRNA gene studies. We also discuss this comparison in terms of the positioning function of the split class III promoter elements and the evolutionary conservation of the spacing between the two promoter elements for optimum transcriptional efficiency.

Quattrochi, L. C., U. R. Pendurthi, S. T. Okino, C. Potenza, and R. H. Tukey. 1986. Human cytochrome P-450 4 mRNA and gene: part of a multigene family that contains Alu sequences in its mRNA. Proc Natl Acad Sci U S A. 83(18):6731-5.

Several overlapping lambda gt11 cDNA clones have been sequenced and shown to encode for the full-length human cytochrome P-450 4. The structure and location of the exons and flanking intron regions were also identified from a lambda EMBL-3 human genomic clone that encodes the full-length human P-450 4 gene. The human P-450 4 mRNA is flanked by 62 base pairs of 5'- and 1508 base pairs of 3'-noncoding sequence, with 1548 bases that encode a protein of 516 amino acids (Mr, 58,376). The predicted amino acid sequence of human P-450 4 is 69% and 70% homologous to its equivalent in mouse and rat, respectively, 75% homologous to rabbit P-450 4, and 68% homologous to human P1-450. The 7.6-kilobase gene encodes 3118 nucleotides of exon sequence that is separated by six introns into seven exons. Exon 7, which is 1802 nucleotides, contains three inverse/complement Alu sequences that are organized in tandem. Comparison of the genomic DNA sequence of the human P-450 4 gene with the human P1-450 and related genes in rat and mouse and the identification of the amino acid residues and triplet codon at each exon-intron junction show that the location of each intron in the human P-450 4 gene is conserved within this gene family. Although the length and homology of the introns within a related gene family may not be conserved, the location of intronic sequences may be an important determinant in the identification of related P-450 genes.

Sawada, I., and C. W. Schmid. 1986. Primate evolution of the alpha-globin gene cluster and its Alu-like repeats. J Mol Biol. 192(4):693-709.

The arrangement of alpha-globin genes in Old World and New World monkeys and a prosimian, galago, has been determined by restriction mapping. Recombinant DNAs containing galago and Old World monkey alpha- globin genes have been isolated and subjected to a partial sequence determination for comparison to alpha-globin genes in human, chimpanzee and non-primate mammals. The results of this extensive structural analysis are relevant to several topics concerning the evolution of primate alpha-globin genes and Alu family repeats. All orders of higher primates (i.e. Old and New World monkeys, chimpanzee and human) have the same arrangement of alpha-globin genes. In contrast, the arrangement and correction of galago alpha-globin genes differ from those of higher primates, but are similar to those of non-primate mammals. The 5' and 3'-flanking regions of the human alpha 1 gene are orthologous to the corresponding region in galago, identifying the human alpha 2 gene as the more recently duplicated gene. The human psi alpha 1 gene is found to be inactivated after divergence of the human and galago lineages but prior to the divergence of human and monkey. Orthologous Alu family members in human and monkey DNAs indicate that the dispersion of some Alu repeats occurred prior to the divergence of these lineages. However, the Alu-like repeats of prosimian and higher primates result from entirely independent events giving rise to different repeat elements inserted at distinct genomic positions.

Siegel, V., and P. Walter. 1986. Removal of the Alu structural domain from signal recognition particle leaves its protein translocation activity intact. Nature. 320(6057):81-4.

Alu-like elements comprise the most abundant family of interspersed repetitive sequences in primates and rodents, and contain many features of processed genes, suggesting that they were initially derived by reverse transcription of processed RNA transcripts. Transcripts containing Alu family members are represented in heterologous nuclear RNAs, cytoplasmic messenger RNAs and small RNAs, although nothing is known about their function. Evolutionary studies strongly suggest that the parent RNA for the Alu-like elements is the highly conserved 7SL RNA, which is an essential component of signal recognition particle (SRP), a small cytoplasmic ribonucleoprotein whose function is the targeting of nascent secretory and membrane proteins to the rough endoplasmic reticulum (for a review see ref. 6). 7SL RNA is composed of both unique and Alu-like sequences. SRP is rod-shaped and, in addition to its RNA, contains four proteins (two monomers composed of a polypeptide of relative molecular mass (Mr) 19,000 (19K) and one of 54K, and two heterodimers, one composed of a 9K and a 14K polypeptide, and the other composed of a 68K and a 72K polypeptide, respectively). The RNA moiety is required for SRP activity, as well as for structural integrity of the particle. To investigate whether the Alu-like segments of 7SL RNA have a specific role in SRP activity, we have now purified and analysed a SRP subparticle that is created upon extensive digestion with micrococcal nuclease and entirely lacks the Alu-like sequences. We find that it contains the 72/68K, 54K and 19K proteins tightly bound, but lacks the 9/14K protein. In vitro activity assays demonstrated that the subparticle could still promote secretory protein translocation across the microsomal membrane, but could no longer trigger an arrest of pre-secretory protein synthesis. Re-addition of the 9/14K protein did not restore the elongation arrest. We conclude that the region of SRP comprised of the Alu-like RNA and the 9/14K protein exists in a distinct structural domain which is not required for the protein translocation promoted by SRP but apparently confers elongation- arresting activity on the particle.

Sun, L. H., and F. R. Frankel. 1986. The induction of Alu-sequence transcripts by glucocorticoid in rat liver cells. J Steroid Biochem. 25(2):201-7.

Two cDNA clones isolated from a library prepared from dexamethasone- treated rat hepatoma cells have permitted us to detect the presence and the induction of heterogeneous, mainly short, RNA molecules in hepatoma cells and in rat liver, but not in several other rat tissues. The induction by dexamethasone is inhibited by 100 X progesterone. Pulse label experiments suggest that it occurs in part at least, at the level of transcription and may be mediated by RNA polymerase III. The induction of the RNAs is stimulated by cycloheximide, even in the absence of hormone, but not significantly by other stressful conditions. One line of hepatoma cells spontaneously lost its ability to induce these RNAs and synthesized them constitutively. These altered cells showed proper induction of another dexamethasone-mediated response, indicating that the glucocorticoid receptor was functionally normal in these cells. The two clones contain a type 2 Alu-like sequence. The short RNAs can be distinguished from 7SL RNA, which also contains Alu-sequences. We hypothesize that the synthesis of these RNAs may be regulated by an inhibitor of transcription which is inactivated by dexamethasone. Accordingly, cycloheximide relieves the inhibition by preventing synthesis of the inhibitor and the altered cell line has spontaneously lost the function of the inhibitor. The function of these RNAs for the cell is not known. We believe this to be the first report of hormone-regulated tissue specific synthesis of repeat-sequence transcripts.

Auwerx, J., H. de Loof, and G. Verhoeven. 1986. Alu sequences in the LDL receptor messenger RNA [letter]. Nature. 321(6072):733-4.

Anachkova, B., G. Russev, and H. Altmann. 1985. Identification of the short dispersed repetitive DNA sequences isolated from the zones of initiation of DNA synthesis in human cells as Alu- elements. Biochem Biophys Res Commun. 128(1):101-6.

DNA of Xeroderma pigmentosum cells was crosslinked in vivo with trioxsalen and long wave length ultraviolet light and the cells were cultured in the presence of labelled thymidine for one hour. The nascent DNA chains synthesized during this period and containing the DNA replication origins were isolated from the high molecular weight chromosomal DNA by an alkaline sucrose density gradient centrifugation. They were 5-10-fold enriched in short dispersed repetitive sequences identified by dot-blot hybridization to BLUR 8 plasmid as members of the human Alu-family.

Daniels, G. R., and P. L. Deininger. 1985. Integration site preferences of the Alu family and similar repetitive DNA sequences. Nucleic Acids Res. 13(24):8939-54.

Numerous flanking nucleotide sequences from two primate interspersed repetitive DNA families have been aligned to determine the integration site preferences of each repetitive family. This analysis indicates that both the human Alu and galago Monomer families were preferentially inserted into short d(A+T)-rich regions. Moreover, both primate repeat families demonstrated an orientation specific integration with respect to dA-rich sequences within the flanking direct repeats. These observations suggest that a common mechanism exists for the insertion of many repetitive DNA families into new genomic sites. A modified mechanism for site-specific integration of primate repetitive DNA sequences is provided which requires insertion into dA-rich sequences in the genome. This model is consistent with the observed relationship between galago Type II subfamilies suggesting that they have arisen not by mere mutation but by independent integration events.

den Dunnen, J. T., R. J. Moormann, F. P. Cremers, and J. G. Schoenmakers. 1985. Two human gamma-crystallin genes are linked and riddled with Alu- repeats. Gene. 38(1-3):197-204.

A human genomic cosmid clone, pHcos gamma-1, has been isolated containing two closely linked gamma-crystallin genes, oriented in the same direction. The sequence of these genes and their 5' and 3' flanking regions has been determined. The coding regions of both genes are interrupted by two introns. The first introns (94 and 100 bp, respectively) are located in the 5' region of the genes. The second introns (2.82 and 0.95 kb, respectively) divide the genes into two halves, each encoding a structural domain of the gamma-crystallin protein. The coding regions of the two genes show 80% homology. Due to a mutation in the splice acceptor site of the second intron of the first gene, the coding region of its third exon is 3 bp longer than that of the second gene. In the flanking regions several conserved sequence elements were found, including those elements that are known to be necessary for the correct expression of eukaryotic genes. The flanking and intronic regions of the genes contain 'simple sequence' DNA and Alu repeats. The Alu repeats are usually clustered, contain truncated elements, and are often located near simple sequence DNA.

Economou-Pachnis, A., and P. N. Tsichlis. 1985. Insertion of an Alu SINE in the human homologue of the Mlvi-2 locus. Nucleic Acids Res. 13(23):8379-87.

Fifty-nine human DNA samples derived from either normal tissues or hematopoietic neoplasias were examined for rearrangements in the Mlvi-2 locus, a putative oncogene. The rearranged Mlvi-2 sequences in one of them, a B cell lymphoma, were shown to result from the insertion of an approximately 300 bp DNA fragment that hybridized to a human Alu probe. DNA sequence analysis of both the rearranged and the nonrearranged allele around the site of the insertion revealed the following: a) the insert was 88.4% homologous to the consensus sequence of the Alu family of repeats and 75% homologous to the Alu related sequence in the human 7SL RNA; b) similar to other sequenced SINES, a poly(d.A) tract was present at the 3' end of this element; c) an 8 bp direct repeat was present at both ends of the inserted element; d) this repeat was present as a single copy in the unrearranged allele. We conclude from these findings that: Alu sequences can transpose and that the direct repeats flanking certain Alu SINES may be generated by the duplication of single copy cellular sequences at the site of the insertion. Furthermore the recent nature of the Alu insertion in the Mlvi-2 locus coupled to the low degree of homology of the inserted Alu to the Alu related sequence in the 7SL RNA suggest that this event did not occur via reverse transcription and reintegration of the 7SL RNA.

Hess, J., C. Perez-Stable, G. J. Wu, B. Weir, I. Tinoco, Jr., and C. K. Shen. 1985. End-to-end transcription of an Alu family repeat. A new type of polymerase-III-dependent terminator and its evolutionary implication. J Mol Biol. 184(1):7-21.

Four or more consecutive thymidine residues on the non-template strand and G + C-richness of flanking DNA are the two necessary characteristics of efficient RNA polymerase-III-dependent transcriptional terminators. We have identified, from the study of in vitro transcription of a human Alu family repeat, a new type of RNA polymerase-III-dependent transcriptional terminator. A 258 base-pair Alu repeat located on the 3' side of the human alpha 1 globin gene can be transcribed in a HeLa S-100 extract to generate three RNA species of lengths 404 to 408, 252 to 255 and 173 to 174 nucleotides, respectively. Kinetics, pulse-chase and RNA incubation experiments showed no significant internal processing of the longer transcripts into shorter ones. These data plus detailed RNA mapping demonstrated conclusively that the multiple Alu RNA species resulted from accurate initiation at the first base (5' end) of the repeat, and multiple termination downstream. The 3' end(s) of the major transcript (252 to 255 nucleotides) maps at the 3' end of the Alu repeat sequence where there are not four or more consecutive thymidine residues on the non- template strand. The functional domain of the terminator has been mapped to a 45 base-pair segment that includes 36 base-pairs of the 3' end sequence of the Alu repeat plus nine base-pairs downstream. The high efficiency of termination (greater than 90%), the lack of consecutive T residues, the richness in A + T content, and the proposed ability of the RNA to form an imperfect hairpin structure in the 3' region of the transcript, thus identify a new type of eukaryotic class III terminator. We compare the structure of this class III terminator with that of the bacterial rho-dependent terminator. We also discuss its implication in the mechanism(s) of amplification and dispersion of Alu sequences in the primate genomes.

Hobbs, H. H., M. A. Lehrman, T. Yamamoto, and D. W. Russell. 1985. Polymorphism and evolution of Alu sequences in the human low density lipoprotein receptor gene [published erratum appears in Proc Natl Acad Sci USA 1986 Mar;83(6):1964]. Proc Natl Acad Sci U S A. 82(22):7651-5.

Two clusters of Alu sequences in the human low density lipoprotein (LDL) receptor gene have been analyzed in detail. One Alu cluster is present within the intron separating exons 15 and 16 of the gene and contains a polymorphic Pvu II site. The presence or absence of this site gives rise to two allelic fragments of 14 and 16.5 kilobases, respectively, in genomic Southern blots using cloned cDNA probes. This DNA polymorphic site is caused by a single adenine to guanine transition within an Alu repetitive element. The second cluster of Alu sequences is located in exon 18 of the LDL receptor gene. Southern blotting of primate DNAs suggests that this cluster became associated with the gene about 30 million years ago. Comparison of bovine DNA sequences, which lack this Alu cluster, with those of the human indicates that the Alu sequences inserted in exon 18 in two independent events.

Kole, R., L. D. Fresco, J. D. Keene, P. L. Cohen, R. A. Eisenberg, and P. G. Andrews. 1985. Alu RNA-protein complexes formed in vitro react with a novel lupus autoantibody. J Biol Chem. 260(21):11781-6.

We have screened sera from patients with systemic lupus erythematosus for reactivity with RNA transcribed in vitro using HeLa whole cell extracts. Sera from 14 out of 114 patients precipitated an RNA transcribed by RNA polymerase III from a plasmid containing an Alu family sequence (i.e. the repetitive DNA sequence that is cut by the Alu restriction enzyme) located upstream from the human gamma G-globin gene. These Alu transcripts were not precipitated by anti-La, anti-Sm, anti-RNP or anti-Ro antibodies, suggesting that Alu RNA was precipitated by a previously undescribed lupus specificity. Analysis of [35S]methionine-labeled immunoprecipitates indicated that Alu RNA binds a protein of about 68 kDa. This protein may be Alu specific since three different Alu transcripts were precipitated by the anti-Alu sera whereas another RNA polymerase III transcript, adenovirus VA I RNA, was not precipitated by the same sera.

Lehrman, M. A., W. J. Schneider, T. C. Sudhof, M. S. Brown, J. L. Goldstein, and D. W. Russell. 1985. Mutation in LDL receptor: Alu-Alu recombination deletes exons encoding transmembrane and cytoplasmic domains. Science. 227(4683):140-6.

The molecular size of the plasma LDL (low density lipoprotein) receptor synthesized by cultured fibroblasts from a patient with the internalization-defective form of familial hypercholesterolemia (FH 274) was smaller by 10,000 daltons than the size of the normal LDL receptor. The segment of the gene encoding the truncated portion of the FH 274 receptor was cloned into bacteriophage lambda. Comparison of the nucleotide sequences of the normal and FH 274 genes revealed a 5- kilobase deletion, which eliminated the exons encoding the membrane- spanning region and the carboxyl terminal cytoplasmic domain of the receptor. The deletion appeared to be caused by a novel intrastrand recombination between two repetitive sequences of the Alu family that were oriented in opposite directions. The truncated receptors lack membrane-spanning regions and cytoplasmic domains; they are largely secreted into the culture medium, but a small fraction remains adherent to the cell surface. The surface-adherent receptors bind LDL, but they are unable to cluster in coated pits, thus explaining the internalization-defective phenotype.

Majello, B., G. La Mantia, A. Simeone, E. Boncinelli, and L. Lania. 1985. Activation of major histocompatibility complex class I mRNA containing an Alu-like repeat in polyoma virus-transformed rat cells. Nature. 314(6010):457-9.

Class I genes of the major histocompatibility complex (MHC) appear to be activated in mouse cells transformed by the DNA tumour virus simian virus 40 (SV40). Conversely, suppression of MHC class I genes has been reported in adenovirus-12-transformed baby kidney rat cells. We have now investigated the expression of genes encoded by the rat MHC locus in rat fibroblast cells transformed by polyoma virus (Py). Using a mouse genomic H-2 clone as a probe in Northern transfer hybridization analysis, we have observed a high level of expression of rat MHC class I messenger RNA in all the transformed rat cell lines analysed. The class I 1.6-kilobase (kb) mRNA activated in Py-transformed rat cells appears to contain an Alu-like type II repeat element, as the same 1.6- kb mRNA is detected using either the H-2 class I sequence or a repetitive Alu-like type II element as a probe. High levels of heterogeneous poly(A)+ transcripts of 0.5-0.8 kb are also observed in Py-transformed rat cells using probes containing an Alu-like type II repetitive element.

Rogers, J. 1985. Oncogene chromosome breakpoints and alu sequences [letter]. Nature. 317(6037):559.

Sawada, I., C. Willard, C. K. Shen, B. Chapman, A. C. Wilson, and C. W. Schmid. 1985. Evolution of Alu family repeats since the divergence of human and chimpanzee. J Mol Evol. 22(4):316-22.

The DNA sequences of three members of the Alu family of repeated sequences located 5' to the chimpanzee alpha 2 gene have been determined. The base sequences of the three corresponding human Alu family repeats have been previously determined, permitting the comparison of identical Alu family members in human and chimpanzee. Here we compare the sequences of seven pairs of chimpanzee and human Alu repeats. In each case, with the exception of minor sequence differences, the identical Alu repeat is located at identical sites in the human and chimpanzee genomes. The Alu repeats diverge at the rate expected for nonselected sequences. Sequence conversion has not replaced any of these 14 Alu family members since the divergence between chimpanzee and human.

Shmookler Reis, R. J., C. K. Lumpkin, Jr., J. R. McGill, K. T. Riabowol, and S. Goldstein. 1985. Amplification of inter-Alu extrachromosomal DNA during cellular ageing: retraction and explanation. Nature. 316(6024):167.

We reported previously the age-dependent appearance of extrachromosomal circular DNA bands hybridizing to a human DNA fragment ('inter-Alu'), isolated from a genomic cluster of AluI repeats. Such bands appeared or increased at late passage in four out of six human fibroblast strains (six out of nine cell expansions); moreover, all DNAs (9/9) obtained from peripheral lymphocytes of aged donors, but none (0/8) from young donors, revealed a non-genomic inter-Alu band at congruent to 4.8 kilobases (kb). Subsequent data extended these numbers to 16/24 aged donors compared with 0/18 young donors. These results were interpreted as evidence of age-dependent DNA rearrangement in normal human cells. We now report that the 'extra' bands were of microbial origin, although clearly occurring in an age-dependent manner.

Adeniyi-Jones, S., and M. Zasloff. 1985. Transcription, processing and nuclear transport of a B1 Alu RNA species complementary to an intron of the murine alpha-fetoprotein gene. Nature. 317(6032):81-4.

The Alu sequence family comprises the major dispersed repeat sequences of rodent and primate genomes, numbering greater than 300,000 copies in the human haploid genome. The function of these elements is unknown. The sequences can be transcribed by RNA polymerase III and represent a substantial fraction of total heterogeneous nuclear RNA. Alu sequences can be found both in the flanking regions and within the transcription units of several well-characterized genes. Here we show that some members of the mouse B1 Alu sequence family encode a small cytoplasmic RNA. The mouse B1 sequence is congruent to 130 nucleotides long and shows homology with the monomeric units of the dimeric 300-nucleotide primate sequence. By means of microinjection studies in the Xenopus laevis oocyte, we have elucidated a novel pathway leading to the appearance of a processed B1-type Alu RNA species in the cytoplasm. The abundance of this small Alu RNA differs between various mouse tissues, suggesting a role in tissue-specific gene expression.