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Recently integrated human Alu repeats: finding needles in the haystack

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Abstract

Alu elements undergo amplification through retroposition and integration into new locations throughout primate genomes. Over 500,000 Alu elements reside in the human genome, making the identification of newly inserted Alu repeats the genomic equivalent of finding needles in the haystack. Here, we present two complementary methods for rapid detection of newly integrated Alu elements. In the first approach we employ computational biology to mine the human genomic DNA sequence databases in order to identify recently integrated Alu elements. The second method is based on an anchor-PCR technique which we term Allele-Specific Alu PCR (ASAP). In this approach, Alu elements are selectively amplified from anchored DNA generating a display or 'fingerprint' of recently integrated Alu elements. Alu insertion polymorphisms are then detected by comparison of the DNA fingerprints generated from different samples. Here, we explore the utility of these methods by applying them to the identification of members of the smallest previously identified subfamily of Alu repeats in the human genome termed Ya8. This subfamily of Alu repeats is composed of about 50 elements within the human genome. Approximately 50% of the Ya8 Alu family members have inserted in the human genome so recently that they are polymorphic, making them useful markers for the study of human evolution.

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References

  • Altschul, S.F., W. Gish, W. Miller, E.W. Myers & D.J. Lipman, 1990. Basic local alignment search tool. J. Mol. Biol. 215: 403–410.

    Article  PubMed  CAS  Google Scholar 

  • Arcot, S.S., T.H. Shaikh, J. Kim, L. Bennett, M. Alegria-Hartman, D.O. Nelson, P.L. Deininger & M.A. Batzer, 1995a. Sequence diversity and chromosomal distribution of ‘young’ Alu repeats. Gene 163: 273–278.

    Article  PubMed  CAS  Google Scholar 

  • Arcot, S.S., Z. Wang, J.L. Weber, P.L. Deininger & M.A. Batzer, 1995b. Alu repeats: A source for the genesis of primate microsatellites. Genomics 29: 136–144.

    Article  PubMed  CAS  Google Scholar 

  • Arcot, S.S., A.W. Adamson, G.W. Risch, J. LaFleur, M.B. Robichaux, J.E. Lamerdin, A.V. Carrano & M.A. Batzer, 1998. High-resolution cartography of recently integrated human chromosome 19-specific Alu fossils. J. Mol. Biol. 281: 843–856.

    Article  PubMed  CAS  Google Scholar 

  • Arcot, S.S., J.J. Fontius, P.L. Deininger & M.A. Batzer, 1995c. Identification and analysis of a ‘young’ polymorphic Alu element. Biochem. Biophys. Acta 1263: 99–102.

    PubMed  Google Scholar 

  • Ausubel, F.M., R. Brent, R.E. Kingston, D.D. Moore, J.G. Seidman, J.A. Smith & K. Struhl, 1996. Current Protocols in Molecular Biology, Wiley, Canada.

    Google Scholar 

  • 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.B. Keats, P.L. Deininger & M. Stoneking, 1996a. Genetic variation of recent Alu insertions in human populations. J. Mol. Evol. 42: 22–29.

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • 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 & C.W. Schmid, 1995. Dispersion and insertion polymorphism in two small subfamilies of recently amplified human Alu repeats. J. Mol. Biol. 247: 418–427.

    Article  PubMed  CAS  Google Scholar 

  • Batzer, M.A., M. Alegria-Hartman, H. Bazan, D.H. Kass, G. Novick, P.A. Ioannou, D. Boudreau, W.D. Scheer, R.J. Herrera, M. Stoneking & P. Deininger, 1994a. Alu repeats as markers for human population genetics. IVth International Symposium on Human Identification, 49–57.

  • Batzer, M.A., M. Stoneking, M. Alegria-Hartman, H. Bazan, D.H. Kass, T.H. Shaikh, G. Novick & P.A. Ioannou, 1994b. African origin of human-specific polymorphic Alu insertions. Proc. Natl. Acad. Sci., USA 91: 12288–12292.

    Article  PubMed  CAS  Google Scholar 

  • Batzer, M.A. & P.L. Deininger, 1991a. A human-specific subfamily of Alu sequences. Genomics 9: 481–487.

    Article  PubMed  CAS  Google Scholar 

  • Batzer, M.A., V. Gudi, J.C. Mena, D.W. Foltz, R.J. Herrera & P.L. Deininger, 1991b. Amplification dynamics of human-specific (HS) Alu family members. Nucleic Acids Res. 19: 3619–3623.

    PubMed  CAS  Google Scholar 

  • Batzer, M.A., G.E. Kilroy, P.L. Richard, T.H. Shaikh, T.D. Desselle, C.L. Hoppens & P.L. Deininger, 1990. Structure and variability of recently inserted Alu family members. Nucleic Acids Res. 18: 6793–6798.

    PubMed  CAS  Google Scholar 

  • Batzer, M.A., C.W. Schmid & P.L. Deininger, 1993. Evolutionary analyses of repetitive DNA sequences. Methods Enzymol. 224: 213–232.

    Article  PubMed  CAS  Google Scholar 

  • Bird, A.P., 1980. DNA methylation and the frequency of CpG in animal DNA. Nucleic. Acids. Res. 8: 1499–1504.

    PubMed  CAS  Google Scholar 

  • Daniels, G. & P.L. Deininger, 1985. Repeat sequence families derived from mammalian tRNA genes. Nature 317: 819–822.

    Article  PubMed  CAS  Google Scholar 

  • Deininger, P.L. & M.A. Batzer, 1995. SINE master genes and population biology, pp. 43–60 in The Impact of Short, Interspersed Elements (SINEs) on the Host Genome, edited by, R. Maraia, R.G. Landes, Georgetown, TX.

  • Deininger, P.L. & M.A. Batzer, 1993. Evolution of Retroposons, pp. 157–196 in Evolutionary Biology edited by M.K. Heckht et al., Plenum Publishing, New York.

    Google Scholar 

  • Deininger, P.L. & M.A. Batzer, 1999. Alu repeats and human disease. Mol. Genet. Metab. 67: 183–193.

    Article  PubMed  CAS  Google Scholar 

  • 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: 749–761.

    PubMed  CAS  Google Scholar 

  • Hutchinson, G.B., S.E. Andrew, H. McDonald, Y.P. Goldberg, R. Graham, J.M. Rommens & M.R. Hayden, 1993. An Alu element retroposition in two families with Huntington disease defines a new active Alu subfamily. Nucleic. Acids. Res. 21: 3379–3383.

    PubMed  CAS  Google Scholar 

  • Jurka, J., P. Klonowski, V. Dagman & P. Pelton, 1996. CENSOR — a program for identification and elimination of repetitive elements from DNA sequences. Computers and Chemistry 20(1): 119–122.

    Article  PubMed  CAS  Google Scholar 

  • Kass, D.H., C. Alemán, M.A. Batzer & P.L. Deininger, 1994. An HS Alu insertion caused a factor XIIIB gene RFLP. Genetica 94: 1–8.

    Article  PubMed  CAS  Google Scholar 

  • Kass, D.H., M.A. Batzer & P.L. Deininger, 1996. Characterization and population diversity of interspersed repeat sequence variants (IRS-morphs). Genome 39: 688–696.

    CAS  PubMed  Google Scholar 

  • Labuda, D. & G. Striker, 1989. Sequence conservation in Alu evolution. Nucleic. Acids. Res. 17: 2477–2491.

    PubMed  CAS  Google Scholar 

  • Miyamoto, M.M., J.L. Slightom & M. Goodman, 1987. Phylogenetic relations of human and African apes from DNA sequences in the psi eta-globin region. Science 238: 369–373.

    PubMed  CAS  Google Scholar 

  • Munroe, D.J., M. Haas, E. Bric, T. Whitton, H. Aburatani, K. Hunter, D. Ward & D.E. Housman, 1994. IRE-bubble PCR: a rapid method for efficient and representative amplification of human genomic DNA sequences from complex sources. Genomics 19: 506–514.

    Article  PubMed  CAS  Google Scholar 

  • Novick, G., T. Gonzalez, J. Garrison, C. Novick, M. Batzer, P. Deininger & R. Herrera, 1993. The use of polymorphic Alu insertions in human DNA fingerprinting, in pp. 283–291 DNA Fingerprinting: State of the science, edited by S.D.J. Pena, R. Chakraborty, J.T. Epplen and A.J. Jeffreys, Birkhauser Verlag, Basel.

    Google Scholar 

  • Perna, N.T., M.A. Batzer, P.L. Deininger & M. Stoneking, 1992. Alu insertion polymorphism: A new type of marker for human population studies. Human Biology 64: 641–648.

    CAS  Google Scholar 

  • Shen, M.R., M.A. Batzer & P.L. Deininger, 1991. Evolution of the Master Alu Gene(s). J. Mol. Evol. 33: 311–320.

    Article  PubMed  CAS  Google Scholar 

  • Stoneking, M., J.J. Fontius, S.L. Clifford, H. Soodyall, S.S. Arcot, N. Saha, T. Jenkins, M.A. Tahir, P.L. Deininger & M.A. Batzer, 1997. Alu insertion polymorphisms and human evolution: evidence for a larger population size in Africa. Genome Res. 7: 1061–1071.

    PubMed  CAS  Google Scholar 

  • Zietkiewicz, E., C. Richer, W. Makalowski, J. Jurka & D. Labuda, 1994. A young Alu subfamily amplified independently in human and African great apes lineages. Nucleic. Acids. Res. 22: 5608–5612.

    PubMed  CAS  Google Scholar 

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Authors and Affiliations

  1. Tulane Cancer Center, SL-66, Department of Environmental Health Sciences, Tulane University -Medical Center, 1430 Tulane Ave., SL-66, New Orleans, LA, 70112, USA

    Astrid M. Roy & Prescott L. Deininger

  2. Departments of Pathology, Biometry and Genetics, Biochemistry and Molecular Biology, Stanley S. Scott Cancer Center, Neuroscience Center of Excellence, Louisiana State University Health Sciences Center, 1901 Perdido Street, New Orleans, LA, 70112, USA

    Marion L. Carroll, Son V. Nguyen, Abdel-Halim Salem & Mark A. Batzer

  3. Department of Biology, Eastern Michigan University, 316 Mark Jefferson, Ypsilanti, MI, 48197, USA

    David H. Kass

  4. Laboratory of Molecular Genetics, Alton OchsnerMedical Foundation, 1516 Jefferson Highway, NewOrleans, 70121

    Prescott L. Deininger

  5. Department of Anatomy, Faculty of Medicine, Suez Canal University, Ismailia, Egypt

    Abdel-Halim Salem

  6. Tulane Cancer Center, Tulane University - Medical Center, 1430 Tulane Ave., SL-66, New Orleans, LA, 70112, USA (Phone: (

    Prescott L. Deininger

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  1. Astrid M. Roy
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  2. Marion L. Carroll
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  4. Son V. Nguyen
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  6. Mark A. Batzer
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  7. Prescott L. Deininger
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Roy, A.M., Carroll, M.L., Kass, D.H. et al. Recently integrated human Alu repeats: finding needles in the haystack. Genetica 107, 149–161 (1999). https://doi.org/10.1023/A:1003941704138

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  • DOI: https://doi.org/10.1023/A:1003941704138

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