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Comparative and Functional Genomics
Volume 2012 (2012), Article ID 947089, 7 pages
http://dx.doi.org/10.1155/2012/947089
Research Article

Transposable Elements Are a Significant Contributor to Tandem Repeats in the Human Genome

Department of Biological Sciences, Brock University, St. Catharines, ON, Canada L2S 3A1

Received 25 February 2012; Revised 10 April 2012; Accepted 11 April 2012

Academic Editor: Yasunori Aizawa

Copyright © 2012 Musaddeque Ahmed and Ping Liang. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. B. Charlesworth, “Genetic recombination: patterns in the genome,” Current Biology, vol. 4, no. 2, pp. 182–184, 1994. View at Publisher · View at Google Scholar · View at Scopus
  2. A. J. Jeffreys, V. Wilson, and S. L. Thein, “Individual-specific “fingerprints” of human DNA,” Nature, vol. 316, no. 6023, pp. 76–79, 1985. View at Google Scholar · View at Scopus
  3. K. Tamaki, X. L. Huang, T. Yamamoto, R. Uchihi, H. Nozawa, and Y. Katsumata, “Applications of minisatellite variant repeat (MVR) mapping for maternal identification from remains of an infant and placenta,” Journal of Forensic Sciences, vol. 40, no. 4, pp. 695–700, 1995. View at Google Scholar · View at Scopus
  4. N. K. Spurr, S. P. Bryant, J. Attwood et al., “European Gene Mapping Project (EUROGEM): genetic maps based on the CEPH reference families,” European Journal of Human Genetics, vol. 2, no. 3, pp. 193–252, 1994. View at Google Scholar · View at Scopus
  5. A. J. Jeffreys and S. D. Pena, “Brief introduction to human DNA fingerprinting,” Experientia, vol. 67, pp. 1–20, 1993. View at Google Scholar · View at Scopus
  6. J. A. L. Armour, T. Anttinen, C. A. May et al., “Minisatellite diversity supports a recent African origin for modern humans,” Nature Genetics, vol. 13, no. 2, pp. 154–160, 1996. View at Publisher · View at Google Scholar · View at Scopus
  7. P. Bois and A. J. Jeffreys, “Minisatellite instability and germline mutation,” Cellular and Molecular Life Sciences, vol. 55, no. 12, pp. 1636–1648, 1999. View at Publisher · View at Google Scholar · View at Scopus
  8. G. R. Sutherland, E. Baker, and R. I. Richards, “Fragile sites still breaking,” Trends in Genetics, vol. 14, no. 12, pp. 501–506, 1998. View at Publisher · View at Google Scholar · View at Scopus
  9. G. Levinson and G. A. Gutman, “Slipped-strand mispairing: a major mechanism for DNA sequence evolution,” Molecular Biology and Evolution, vol. 4, no. 3, pp. 203–221, 1987. View at Google Scholar · View at Scopus
  10. P. R. J. Bois, “Hypermutable minisatellites, a human affair?” Genomics, vol. 81, no. 4, pp. 349–355, 2003. View at Publisher · View at Google Scholar · View at Scopus
  11. J. Murray, J. Buard, D. L. Neil et al., “Comparative sequence analysis of human minisatellites showing meiotic repeat instability,” Genome Research, vol. 9, no. 2, pp. 130–136, 1999. View at Google Scholar · View at Scopus
  12. G. F. Richard and F. Pâques, “Mini- and microsatellite expansions: the recombination connection,” EMBO Reports, vol. 1, no. 2, pp. 122–126, 2000. View at Google Scholar · View at Scopus
  13. A. J. Jeffreys, K. Tamaki, A. MacLeod, D. G. Monckton, D. L. Neil, and J. A. L. Armour, “Complex gene conversion events in germline mutation at human minisatellites,” Nature Genetics, vol. 6, no. 2, pp. 136–145, 1994. View at Publisher · View at Google Scholar · View at Scopus
  14. J. S. Taylor and F. Breden, “Slipped-strand mispairing at noncontiguous repeats in Poecilia reticulata: a model for minisatellite birth,” Genetics, vol. 155, no. 3, pp. 1313–1320, 2000. View at Google Scholar · View at Scopus
  15. J. E. Haber and E. J. Louis, “Minisatellite origins in yeast and humans,” Genomics, vol. 48, no. 1, pp. 132–135, 1998. View at Publisher · View at Google Scholar · View at Scopus
  16. R. E. Mills, E. A. Bennett, R. C. Iskow, and S. E. Devine, “Which transposable elements are active in the human genome?” Trends in Genetics, vol. 23, no. 4, pp. 183–191, 2007. View at Publisher · View at Google Scholar · View at Scopus
  17. D. J. Hedges, P. A. Callinan, R. Cordaux, J. Xing, E. Barnes, and M. A. Batzer, “Differential Alu mobilization and polymorphism among the human and chimpanzee lineages,” Genome Research, vol. 14, no. 6, pp. 1068–1075, 2004. View at Publisher · View at Google Scholar · View at Scopus
  18. R. E. Mills, E. A. Bennett, R. C. Iskow et al., “Recently mobilized transposons in the human and chimpanzee genomes,” American Journal of Human Genetics, vol. 78, no. 4, pp. 671–679, 2006. View at Publisher · View at Google Scholar · View at Scopus
  19. H. Watanabe, A. Fujiyama, M. Hattori, T. Taylor, A. Toyoda, and Y. Kuroki, “DNA sequence and comparative analysis of chimpanzee chromosome 22,” Nature, vol. 429, no. 6990, pp. 382–388, 2004. View at Google Scholar
  20. J. Wang, L. Song, M. K. Gonder et al., “Whole genome computational comparative genomics: a fruitful approach for ascertaining Alu insertion polymorphisms,” Gene, vol. 365, no. 1-2, pp. 11–20, 2006. View at Publisher · View at Google Scholar · View at Scopus
  21. J. Jurka and A. J. Gentles, “Origin and diversification of minisatellites derived from human Alu sequences,” Gene, vol. 365, no. 1-2, pp. 21–26, 2006. View at Publisher · View at Google Scholar · View at Scopus
  22. D. Ames, N. Murphy, T. Helentjaris, N. Sun, and V. Chandler, “Comparative analyses of human single- and multilocus tandem repeats,” Genetics, vol. 179, no. 3, pp. 1693–1704, 2008. View at Publisher · View at Google Scholar · View at Scopus
  23. Y. Gelfand, A. Rodriguez, and G. Benson, “TRDB—the tandem repeats database,” Nucleic Acids Research, vol. 35, no. 1, pp. D80–D87, 2007. View at Publisher · View at Google Scholar · View at Scopus
  24. J. Jurka, V. V. Kapitonov, A. Pavlicek, P. Klonowski, O. Kohany, and J. Walichiewicz, “Repbase Update, a database of eukaryotic repetitive elements,” Cytogenetic and Genome Research, vol. 110, no. 1–4, pp. 462–467, 2005. View at Publisher · View at Google Scholar · View at Scopus
  25. R. Chenna, H. Sugawara, T. Koike et al., “Multiple sequence alignment with the Clustal series of programs,” Nucleic Acids Research, vol. 31, no. 13, pp. 3497–3500, 2003. View at Publisher · View at Google Scholar · View at Scopus
  26. V. Kapitonov and J. Jurka, “The age of Alu subfamilies,” Journal of Molecular Evolution, vol. 42, no. 1, pp. 59–65, 1996. View at Publisher · View at Google Scholar · View at Scopus
  27. G. Churakov, N. Grundmann, A. Kuritzin, J. Brosius, W. Makaowski, and J. Schmitz, “A novel web-based TinT application and the chronology of the Primate Alu retroposon activity,” BMC Evolutionary Biology, vol. 10, no. 1, article 376, 2010. View at Publisher · View at Google Scholar · View at Scopus
  28. S. Nishizawa, T. Kubo, and T. Mikami, “Variable number of tandem repeat loci in the mitochondrial genomes of beets,” Current Genetics, vol. 37, no. 1, pp. 34–38, 2000. View at Google Scholar · View at Scopus
  29. M. Babcock, A. Pavlicek, E. Spiteri et al., “Shuffling of genes within low-copy repeats on 22q11 (LCR22) by Alu-mediated recombination events during evolution,” Genome Research, vol. 13, no. 12, pp. 2519–2532, 2003. View at Publisher · View at Google Scholar · View at Scopus
  30. A. J. Gentles, O. Kohany, and J. Jurka, “Evolutionary diversity and potential recombinogenic role of integration targets of non-LTR retrotransposons,” Molecular Biology and Evolution, vol. 22, no. 10, pp. 1983–1991, 2005. View at Publisher · View at Google Scholar · View at Scopus
  31. J. Jurka, P. Klonowski, and E. N. Trifonov, “Mammalian retroposons integrate at kinkable DNA sites,” Journal of Biomolecular Structure and Dynamics, vol. 15, no. 4, pp. 717–721, 1998. View at Google Scholar · View at Scopus
  32. T. D. Mashkova, N. Y. Oparina, M. H. Lacroix et al., “Structural rearrangements and insertions of dispersed elements in pericentromeric alpha satellites occur preferably at kinkable DNA sites,” Journal of Molecular Biology, vol. 305, no. 1, pp. 33–48, 2001. View at Publisher · View at Google Scholar · View at Scopus