About this Journal Submit a Manuscript Table of Contents 
Comparative and Functional Genomics
Volume 2012 (2012), Article ID 129416, 8 pages
doi:10.1155/2012/129416
Research Article

High Levels of Sequence Diversity in the 5′ UTRs of Human-Specific L1 Elements

Jungnam Lee,1 Seyoung Mun,2 Thomas J. Meyer,3 and Kyudong Han1

1Department of Nanobiomedical Science & WCU Research Center, Dankook University, Cheonan 330-714, Republic of Korea
2Department of Microbiology, College of Advance Science, Dankook University, Cheonan 330-714, Republic of Korea
3Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA

Received 29 July 2011; Revised 25 October 2011; Accepted 31 October 2011

Academic Editor: Brian Wigdahl

Copyright © 2012 Jungnam Lee et al. 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. E. S. Lander, L. M. Linton, B. Birren et al., “Initial sequencing and analysis of the human genome,” Nature, vol. 409, no. 6822, pp. 860–921, 2001. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  2. P. L. Deininger and M. A. Batzer, “Alu repeats and human disease,” Molecular Genetics and Metabolism, vol. 67, no. 3, pp. 183–193, 1999. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  3. P. A. Callinan, J. Wang, S. W. Herke, R. K. Garber, P. Liang, and M. A. Batzer, “Alu retrotransposition-mediated deletion,” Journal of Molecular Biology, vol. 348, no. 4, pp. 791–800, 2005. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  4. D. E. Symer, C. Connelly, S. T. Szak et al., “Human L1 retrotransposition is associated with genetic instability in vivo,” Cell, vol. 110, no. 3, pp. 327–338, 2002. View at Publisher · View at Google Scholar · View at Scopus
  5. N. Gilbert, S. Lutz-Prigge, and J. V. Moran, “Genomic deletions created upon LINE-1 retrotransposition,” Cell, vol. 110, no. 3, pp. 315–325, 2002. View at Publisher · View at Google Scholar · View at Scopus
  6. K. Han, S. K. Sen, J. Wang et al., “Genomic rearrangements by LINE-1 insertion-mediated deletion in the human and chimpanzee lineages,” Nucleic Acids Research, vol. 33, no. 13, pp. 4040–4052, 2005. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  7. S. K. Sen, K. Han, J. Wang et al., “Human genomic deletions mediated by recombination between Alu elements,” The American Journal of Human Genetics, vol. 79, no. 1, pp. 41–53, 2006. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  8. J. Xing, H. Wang, V. P. Belancio, R. Cordaux, P. L. Deininger, and M. A. Batzer, “Emergence of primate genes by retrotransposon-mediated sequence transduction,” Proceedings of the National Academy of Sciences of the United States of America, vol. 103, no. 47, pp. 17608–17613, 2006. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  9. J. M. Chen, P. D. Stenson, D. N. Cooper, and C. Férec, “A systematic analysis of LINE-1 endonuclease-dependent retrotranspositional events causing human genetic disease,” Human Genetics, vol. 117, no. 5, pp. 411–427, 2005. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  10. P. L. Deininger and M. A. Batzer, “Mammalian retroelements,” Genome Research, vol. 12, no. 10, pp. 1455–1465, 2002. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  11. H. H. Kazazian Jr., “Mobile elements: drivers of genome evolution,” Science, vol. 303, no. 5664, pp. 1626–1632, 2004. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  12. A. F. Smit, “The origin of interspersed repeats in the human genome,” Current Opinion in Genetics and Development, vol. 6, no. 6, pp. 743–748, 1996. View at Publisher · View at Google Scholar · View at Scopus
  13. H. H. Kazazian Jr. and J. V. Moran, “The impact of L1 retrotransposons on the human genome,” Nature Genetics, vol. 19, no. 1, pp. 19–24, 1998. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  14. Q. Feng, J. V. Moran, H. H. Kazazian Jr., and J. D. Boeke, “Human L1 retrotransposon encodes a conserved endonuclease required for retrotransposition,” Cell, vol. 87, no. 5, pp. 905–916, 1996. View at Publisher · View at Google Scholar · View at Scopus
  15. V. O. Kolosha and S. L. Martin, “In vitro properties of the first ORF protein from mouse LINE-1 support its role in ribonucleoprotein particle formation during retrotransposition,” Proceedings of the National Academy of Sciences of the United States of America, vol. 94, no. 19, pp. 10155–10160, 1997. View at Publisher · View at Google Scholar · View at Scopus
  16. S. L. Mathias, A. F. Scott, H. H. Kazazian Jr., J. D. Boeke, and A. Gabriel, “Reverse transcriptase encoded by a human transposable element,” Science, vol. 254, no. 5039, pp. 1808–1810, 1991. View at Scopus
  17. T. G. Fanning and M. F. Singer, “LINE-1: a mammalian transposable element,” Biochimica et Biophysica Acta, vol. 910, no. 3, pp. 203–212, 1987. View at Scopus
  18. D. D. Luan, M. H. Korman, J. L. Jakubczak, and T. H. Eickbush, “Reverse transcription of R2Bm RNA is primed by a nick at the chromosomal target site: a mechanism for non-LTR retrotransposition,” Cell, vol. 72, no. 4, pp. 595–605, 1993. View at Publisher · View at Google Scholar · View at Scopus
  19. A. F. Smit, G. Toth, A. D. Riggs, and J. Jurka, “Ancestral, mammalian-wide subfamilies of LINE-1 repetitive sequences,” Journal of Molecular Biology, vol. 246, no. 3, pp. 401–417, 1995. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  20. S. T. Szak, O. K. Pickeral, W. Makalowski, M. S. Boguski, D. Landsman, and J. D. Boeke, “Molecular archeology of L1 insertions in the human genome,” Genome Biology, vol. 3, no. 10, research 0052, 2002.
  21. J. N. Athanikar, R. M. Badge, and J. V. Moran, “A YY1-binding site is required for accurate human LINE-1 transcription initiation,” Nucleic Acids Research, vol. 32, no. 13, pp. 3846–3855, 2004. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  22. H. Khan, A. Smit, and S. Boissinot, “Molecular evolution and tempo of amplification of human LINE-1 retrotransposons since the origin of primates,” Genome Research, vol. 16, no. 1, pp. 78–87, 2006. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  23. J. Lee, R. Cordaux, K. Han et al., “Different evolutionary fates of recently integrated human and chimpanzee LINE-1 retrotransposons,” Gene, vol. 390, no. 1-2, pp. 18–27, 2007. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  24. R. E. Mills, E. A. Bennett, R. C. Iskow et al., “Recently mobilized transposons in the human and chimpanzee genomes,” The American Journal of Human Genetics, vol. 78, no. 4, pp. 671–679, 2006. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  25. B. Brouha, J. Schustak, R. M. Badge et al., “Hot L1s account for the bulk of retrotransposition in the human population,” Proceedings of the National Academy of Sciences of the United States of America, vol. 100, no. 9, pp. 5280–5285, 2003. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  26. W. J. Kent, “BLAT—the BLAST-like alignment tool,” Genome Research, vol. 12, no. 4, pp. 656–664, 2002. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  27. T. A. Hall, “BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT,” Nucleic Acids Symposium Series, vol. 41, pp. 95–98, 1999.
  28. T. Penzkofer, T. Dandekar, and T. Zemojtel, “L1Base: from functional annotation to prediction of active LINE-1 elements,” Nucleic Acids Research, vol. 33, pp. D498–D500, 2005. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  29. H. J. Bandelt, P. Forster, and A. Röhl, “Median-joining networks for inferring intraspecific phylogenies,” Molecular Biology and Evolution, vol. 16, no. 1, pp. 37–48, 1999. View at Scopus
  30. R. Cordaux, D. J. Hedges, and M. A. Batzer, “Retrotransposition of Alu elements: how many sources?” Trends in Genetics, vol. 20, no. 10, pp. 464–467, 2004. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  31. M. M. Miyamoto, J. L. Slightom, and M. Goodman, “Phylogenetic relations of humans and African apes from DNA sequences in the psi eta-globin region,” Science, vol. 238, no. 4825, pp. 369–373, 1987. View at Scopus
  32. L. Lavie, E. Maldener, B. Brouha, E. U. Meese, and J. Mayer, “The human L1 promoter: variable transcription initiation sites and a major impact of upstream flanking sequence on promoter activity,” Genome Research, vol. 14, no. 11, pp. 2253–2260, 2004. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  33. E. Pascale, C. Liu, E. Valle, K. Usdin, and A. V. Furano, “The evolution of long interspersed repeated DNA (L1, LINE 1) as revealed by the analysis of an ancient rodent L1 DNA family,” Journal of Molecular Evolution, vol. 36, no. 1, pp. 9–20, 1993. View at Scopus
  34. C. F. Voliva, S. L. Martin, C. A. Hutchison III, and M. H. Edgell, “Dispersal process associated with the L1 family of interspersed repetitive DNA sequences,” Journal of Molecular Biology, vol. 178, no. 4, pp. 795–813, 1984. View at Scopus
  35. B. L. Welch, “The generalisation of student's problems when several different population variances are involved,” Biometrika, vol. 34, pp. 28–35, 1947.
  36. J. Sved and A. Bird, “The expected equilibrium of the CpG dinucleotide in vertebrate genomes under a mutation model,” Proceedings of the National Academy of Sciences of the United States of America, vol. 87, no. 12, pp. 4692–4696, 1990. View at Publisher · View at Google Scholar · View at Scopus
  37. R. Anbazhagan, J. G. Herman, K. Enika, and E. Gabrielson, “Spreadsheet-based program for the analysis of DNA methylation,” BioTechniques, vol. 30, no. 1, pp. 110–114, 2001. View at Scopus
  38. K. J. Fryxell and W. J. Moon, “CpG mutation rates in the human genome are highly dependent on local GC content,” Molecular Biology and Evolution, vol. 22, no. 3, pp. 650–658, 2005. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  39. M. Li and S. S. Chen, “The tendency to recreate ancestral CG dinucleotides in the human genome,” BMC Evolutionary Biology, vol. 11, article 3, 2011. View at Publisher · View at Google Scholar · View at PubMed
  40. M. Gardiner-Garden and M. Frommer, “CpG islands in vertebrate genomes,” Journal of Molecular Biology, vol. 196, no. 2, pp. 261–282, 1987. View at Scopus
  41. D. Takai and P. A. Jones, “Comprehensive analysis of CpG islands in human chromosomes 21 and 22,” Proceedings of the National Academy of Sciences of the United States of America, vol. 99, no. 6, pp. 3740–3745, 2002. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus