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.
Similar content being viewed by others
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
Batzer, M.A. & P.L. Deininger, 1991a. A human-specific subfamily of Alu sequences. Genomics 9: 481–487.
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.
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.
Batzer, M.A., C.W. Schmid & P.L. Deininger, 1993. Evolutionary analyses of repetitive DNA sequences. Methods Enzymol. 224: 213–232.
Bird, A.P., 1980. DNA methylation and the frequency of CpG in animal DNA. Nucleic. Acids. Res. 8: 1499–1504.
Daniels, G. & P.L. Deininger, 1985. Repeat sequence families derived from mammalian tRNA genes. Nature 317: 819–822.
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.
Deininger, P.L. & M.A. Batzer, 1999. Alu repeats and human disease. Mol. Genet. Metab. 67: 183–193.
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.
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.
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.
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.
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.
Labuda, D. & G. Striker, 1989. Sequence conservation in Alu evolution. Nucleic. Acids. Res. 17: 2477–2491.
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.
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.
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.
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.
Shen, M.R., M.A. Batzer & P.L. Deininger, 1991. Evolution of the Master Alu Gene(s). J. Mol. Evol. 33: 311–320.
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.
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.
Author information
Authors and Affiliations
Rights and permissions
About this article
Cite this article
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
Issue Date:
DOI: https://doi.org/10.1023/A:1003941704138