Skip to main content
PMC home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1991 Jul 11;19(13):3619–3623. doi: 10.1093/nar/19.13.3619

Amplification dynamics of human-specific (HS) Alu family members.

M A Batzer 1, V A Gudi 1, J C Mena 1, D W Foltz 1, R J Herrera 1, P L Deininger 1
PMCID: PMC328388  PMID: 1649453

Abstract

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.

Full text

PDF
3619

Images in this article

3620Image
on p.3620
3621Image
on p.3621

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Antonarakis S. E., Oettgen P., Chakravarti A., Halloran S. L., Hudson R. R., Feisee L., Karathanasis S. K. DNA polymorphism haplotypes of the human apolipoprotein APOA1-APOC3-APOA4 gene cluster. Hum Genet. 1988 Nov;80(3):265–273. doi: 10.1007/BF01790095. [DOI] [PubMed] [Google Scholar]
  2. Batzer M. A., Deininger P. L. A human-specific subfamily of Alu sequences. Genomics. 1991 Mar;9(3):481–487. doi: 10.1016/0888-7543(91)90414-a. [DOI] [PubMed] [Google Scholar]
  3. Batzer M. A., Kilroy G. E., Richard P. E., Shaikh T. H., Desselle T. D., Hoppens C. L., Deininger P. L. Structure and variability of recently inserted Alu family members. Nucleic Acids Res. 1990 Dec 11;18(23):6793–6798. doi: 10.1093/nar/18.23.6793. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Botstein D., White R. L., Skolnick M., Davis R. W. Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet. 1980 May;32(3):314–331. [PMC free article] [PubMed] [Google Scholar]
  5. Britten R. J., Baron W. F., Stout D. B., Davidson E. H. Sources and evolution of human Alu repeated sequences. Proc Natl Acad Sci U S A. 1988 Jul;85(13):4770–4774. doi: 10.1073/pnas.85.13.4770. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Cann R. L., Stoneking M., Wilson A. C. Mitochondrial DNA and human evolution. Nature. 1987 Jan 1;325(6099):31–36. doi: 10.1038/325031a0. [DOI] [PubMed] [Google Scholar]
  7. Daniels G. R., Deininger P. L. Integration site preferences of the Alu family and similar repetitive DNA sequences. Nucleic Acids Res. 1985 Dec 20;13(24):8939–8954. doi: 10.1093/nar/13.24.8939. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Degen S. J., Rajput B., Reich E. The human tissue plasminogen activator gene. J Biol Chem. 1986 May 25;261(15):6972–6985. [PubMed] [Google Scholar]
  9. Deininger P. L., Jolly D. J., Rubin C. M., Friedmann T., Schmid C. W. Base sequence studies of 300 nucleotide renatured repeated human DNA clones. J Mol Biol. 1981 Sep 5;151(1):17–33. doi: 10.1016/0022-2836(81)90219-9. [DOI] [PubMed] [Google Scholar]
  10. Deininger P. L., Slagel V. K. Recently amplified Alu family members share a common parental Alu sequence. Mol Cell Biol. 1988 Oct;8(10):4566–4569. doi: 10.1128/mcb.8.10.4566. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Economou-Pachnis A., Tsichlis P. N. Insertion of an Alu SINE in the human homologue of the Mlvi-2 locus. Nucleic Acids Res. 1985 Dec 9;13(23):8379–8387. doi: 10.1093/nar/13.23.8379. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Economou E. P., Bergen A. W., Warren A. C., Antonarakis S. E. The polydeoxyadenylate tract of Alu repetitive elements is polymorphic in the human genome. Proc Natl Acad Sci U S A. 1990 Apr;87(8):2951–2954. doi: 10.1073/pnas.87.8.2951. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Flemington E., Bradshaw H. D., Jr, Traina-Dorge V., Slagel V., Deininger P. L. Sequence, structure and promoter characterization of the human thymidine kinase gene. Gene. 1987;52(2-3):267–277. doi: 10.1016/0378-1119(87)90053-9. [DOI] [PubMed] [Google Scholar]
  14. Jurka J., Smith T. A fundamental division in the Alu family of repeated sequences. Proc Natl Acad Sci U S A. 1988 Jul;85(13):4775–4778. doi: 10.1073/pnas.85.13.4775. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Kariya Y., Kato K., Hayashizaki Y., Himeno S., Tarui S., Matsubara K. Revision of consensus sequence of human Alu repeats--a review. Gene. 1987;53(1):1–10. doi: 10.1016/0378-1119(87)90087-4. [DOI] [PubMed] [Google Scholar]
  16. Koop B. F., Miyamoto M. M., Embury J. E., Goodman M., Czelusniak J., Slightom J. L. Nucleotide sequence and evolution of the orangutan epsilon globin gene region and surrounding Alu repeats. J Mol Evol. 1986;24(1-2):94–102. doi: 10.1007/BF02099956. [DOI] [PubMed] [Google Scholar]
  17. Labuda D., Striker G. Sequence conservation in Alu evolution. Nucleic Acids Res. 1989 Apr 11;17(7):2477–2491. doi: 10.1093/nar/17.7.2477. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Lee M. G., Loomis C., Cowan N. J. Sequence of an expressed human beta-tubulin gene containing ten Alu family members. Nucleic Acids Res. 1984 Jul 25;12(14):5823–5836. doi: 10.1093/nar/12.14.5823. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Lipman D. J., Pearson W. R. Rapid and sensitive protein similarity searches. Science. 1985 Mar 22;227(4693):1435–1441. doi: 10.1126/science.2983426. [DOI] [PubMed] [Google Scholar]
  20. Matera A. G., Hellmann U., Hintz M. F., Schmid C. W. Recently transposed Alu repeats result from multiple source genes. Nucleic Acids Res. 1990 Oct 25;18(20):6019–6023. doi: 10.1093/nar/18.20.6019. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Matera A. G., Hellmann U., Schmid C. W. A transpositionally and transcriptionally competent Alu subfamily. Mol Cell Biol. 1990 Oct;10(10):5424–5432. doi: 10.1128/mcb.10.10.5424. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Mietus-Snyder M., Charmley P., Korf B., Ladias J. A., Gatti R. A., Karathanasis S. K. Genetic linkage of the human apolipoprotein AI-CIII-AIV gene cluster and the neural cell adhesion molecule (NCAM) gene. Genomics. 1990 Aug;7(4):633–637. doi: 10.1016/0888-7543(90)90211-c. [DOI] [PubMed] [Google Scholar]
  23. Miyamoto M. M., Slightom J. L., Goodman M. Phylogenetic relations of humans and African apes from DNA sequences in the psi eta-globin region. Science. 1987 Oct 16;238(4825):369–373. doi: 10.1126/science.3116671. [DOI] [PubMed] [Google Scholar]
  24. Nakamura Y., Leppert M., O'Connell P., Wolff R., Holm T., Culver M., Martin C., Fujimoto E., Hoff M., Kumlin E. Variable number of tandem repeat (VNTR) markers for human gene mapping. Science. 1987 Mar 27;235(4796):1616–1622. doi: 10.1126/science.3029872. [DOI] [PubMed] [Google Scholar]
  25. Quentin Y. The Alu family developed through successive waves of fixation closely connected with primate lineage history. J Mol Evol. 1988;27(3):194–202. doi: 10.1007/BF02100074. [DOI] [PubMed] [Google Scholar]
  26. Rogers J. Retroposons defined. Nature. 1983 Feb 10;301(5900):460–460. doi: 10.1038/301460e0. [DOI] [PubMed] [Google Scholar]
  27. Sawada I., Schmid C. W. Primate evolution of the alpha-globin gene cluster and its Alu-like repeats. J Mol Biol. 1986 Dec 20;192(4):693–709. doi: 10.1016/0022-2836(86)90022-7. [DOI] [PubMed] [Google Scholar]
  28. Sawada I., Willard C., Shen C. K., Chapman B., Wilson A. C., Schmid C. W. Evolution of Alu family repeats since the divergence of human and chimpanzee. J Mol Evol. 1985;22(4):316–322. doi: 10.1007/BF02115687. [DOI] [PubMed] [Google Scholar]
  29. Slagel V., Flemington E., Traina-Dorge V., Bradshaw H., Deininger P. Clustering and subfamily relationships of the Alu family in the human genome. Mol Biol Evol. 1987 Jan;4(1):19–29. doi: 10.1093/oxfordjournals.molbev.a040422. [DOI] [PubMed] [Google Scholar]
  30. Stoppa-Lyonnet D., Carter P. E., Meo T., Tosi M. Clusters of intragenic Alu repeats predispose the human C1 inhibitor locus to deleterious rearrangements. Proc Natl Acad Sci U S A. 1990 Feb;87(4):1551–1555. doi: 10.1073/pnas.87.4.1551. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Ullu E., Murphy S., Melli M. Human 7SL RNA consists of a 140 nucleotide middle-repetitive sequence inserted in an alu sequence. Cell. 1982 May;29(1):195–202. doi: 10.1016/0092-8674(82)90103-9. [DOI] [PubMed] [Google Scholar]
  32. Weiner A. M., Deininger P. L., Efstratiadis A. Nonviral retroposons: genes, pseudogenes, and transposable elements generated by the reverse flow of genetic information. Annu Rev Biochem. 1986;55:631–661. doi: 10.1146/annurev.bi.55.070186.003215. [DOI] [PubMed] [Google Scholar]
  33. Willard C., Nguyen H. T., Schmid C. W. Existence of at least three distinct Alu subfamilies. J Mol Evol. 1987;26(3):180–186. doi: 10.1007/BF02099850. [DOI] [PubMed] [Google Scholar]

Articles from Nucleic Acids Research are provided here courtesy of Oxford University Press

RESOURCES