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A functional analysis of retroviral endogenous inserts in view of human genome evolution

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Abstract

Retroelements, mobile elements produced in DNA by reverse transcription, comprise about 40% of the human genome. A small part of these elements appeared in the genome quite recently after the divergence of humans and chimpanzees had occurred. Evolutionarily young retroelements are represented by the members of four groups, SVA, Alu, L1, and the endogenous HERV-K (HML-2) virus. These retroelements could play a functional role in the course of the molecular evolution of human DNA. We comprehensively studied the contribution of human-specific endogenous viruses (hsERV) to the structural modifications and regulation of the human genome. We found that hsERV presented in 134 copies occupied about 330000 bp of human DNA. They added to genomic sequences the copies of 50 functional retroviral genes as well as 134 potential promoters and enhancers, 50% of which are located in the regions adjacent to known genes, and 22% in gene introns. At least 67% of these elements are human-specific promoters in vivo. hsERV viruses regulate the activity of known protein-encoding genes by means of RNA interference, function as enhancers, and provide new polyadenylation signals for mRNA.

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Abbreviations

ERV:

endogenous retrovirus

PCR:

polymerase chain reaction

hs:

specific to human DNA, LTR, long terminal repeats

RE:

retroelements

RT PCR:

polymerase chain reaction using reverse transcription

References

  1. Ebersberger, I., Metzler, D., Schwarz, C., and Paabo, S., Am. J. Hum. Genet., 2002, vol. 70, pp. 1490–1497.

    Article  CAS  PubMed  Google Scholar 

  2. Goodman, M., Am. J. Hum. Genet., 1999, vol. 64, pp. 31–39.

    Article  CAS  PubMed  Google Scholar 

  3. Haile-Selassie, Y., Nature, 2001, vol. 412, pp. 178–181.

    Article  CAS  PubMed  Google Scholar 

  4. Buzdin, A., Current Pharmacogenomics, 2006, vol. 4, pp. 1–8.

    Article  CAS  Google Scholar 

  5. Buzdin, A.A., Cell. Mol. Life Sci., 2004, vol. 61, pp. 2046–2059.

    Article  CAS  PubMed  Google Scholar 

  6. Mills, R.E., Bennett, E.A., Iskow, R.C., Luttig, C.T., Tsui, C., Pittard, W.S., and Devine, S.E., Am. J. Hum. Genet., 2006, vol. 78, pp. 671–679.

    Article  CAS  PubMed  Google Scholar 

  7. International Human Genome Sequencing Consortium. Nature, 2001, vol. 409, pp. 860–921.

    Article  Google Scholar 

  8. King, C. and Wilson, C., Science, 1975, vol. 188, pp. 107–116.

    Article  CAS  PubMed  Google Scholar 

  9. Chimpanzee Genome Sequencing Consortium. Nature, 2005, vol. 437, pp. 69–87.

    Article  Google Scholar 

  10. Prabhakar, S., Noonan, J.P., Paabo, S., and Rubin, E.M., Science, 2006, vol. 314, p. 786.

    Article  CAS  PubMed  Google Scholar 

  11. Yunis, J.J. and Prakash, O., Science, 1982, vol. 215, pp. 1525–1530.

    Article  CAS  PubMed  Google Scholar 

  12. Nickerson, E. and Nelson, D.L., Genomics, 1998, vol. 50, pp. 368–372.

    Article  CAS  PubMed  Google Scholar 

  13. Meneveri, R., Agresti, A., Rocchi, M., Marozzi, A., and Ginelli, E., J. Mol. Evol., 1995, vol. 40, pp. 405–412.

    Article  CAS  PubMed  Google Scholar 

  14. Horvath, J.E., Viggiano, L., Loftus, B.J., Adams, M.D., Archidiacono, N., Rocchi, M., and Eichler, E.E., Hum. Mol. Genet., 2000, vol. 9, pp. 113–123.

    Article  CAS  PubMed  Google Scholar 

  15. Royle, N.J., Baird, D.M., and Jeffreys, A.J., Nat. Genet., 1994, vol. 6, pp. 52–56.

    Article  CAS  PubMed  Google Scholar 

  16. Glaser, B., Yen, P.H., and Schempp, W., Chromosome Res., 1998, vol. 6, pp. 481–486.

    Article  CAS  PubMed  Google Scholar 

  17. Kehrer-Sawatzki, H. and Cooper, D.N., Hum. Genet., 2007, vol. 120, pp. 759–778.

    Article  CAS  PubMed  Google Scholar 

  18. Chou, H.H., Takematsu, H., Diaz, S., Iber, J., Nickerson, E., Wright, K.L., Muchmore, E.A., Nelson, D.L., Warren, S.T., and Varki, A., Proc. Natl. Acad. Sci. USA, 1998, vol. 95, pp. 11751–11756.

    Article  CAS  PubMed  Google Scholar 

  19. Gilad, Y., Man, O., Paabo, S., and Lancet, D., Proc. Natl. Acad. Sci. USA, 2003, vol. 100, pp. 3324–3327.

    Article  CAS  PubMed  Google Scholar 

  20. Yu, H., Jiang, H., Zhou, Q., Yang, J., Cun, Y., Su, B., Xiao, C., and Wang, W., Hum. Mol. Genet., 2006, vol. 15, pp. 1870–1875.

    Article  CAS  PubMed  Google Scholar 

  21. Gagneux, P. and Varki, A., Mol. Phylogenet. Evol., 2001, vol. 18, pp. 2–13.

    Article  CAS  PubMed  Google Scholar 

  22. Zimonjic, D.B., Kelley, M.J., Rubin, J.S., Aaronson, S.A., and Popescu, N.C., Proc. Natl. Acad. Sci. USA, 1997, vol. 94, pp. 11461–11465.

    Article  CAS  PubMed  Google Scholar 

  23. Lane, R.P., Cutforth, T., Young, J., Athanasiou, M., Friedman, C., Rowen, L., Evans, G., Axel, R., Hood, L., and Trask, B.J., Proc. Natl. Acad. Sci. USA, 2001, vol. 98, pp. 7390–7395.

    Article  CAS  PubMed  Google Scholar 

  24. Livak, K.J., Rogers, J., and Lichter, J.B., Proc. Natl. Acad. Sci. USA, 1995, vol. 92, pp. 427–431.

    Article  CAS  PubMed  Google Scholar 

  25. Nadezhdin, E.V., Vinogradova, T.V., and Sverdlov, E.D., Dokl. Biochem. Biophys., 2001, vol. 381, pp. 415–418.

    Article  CAS  PubMed  Google Scholar 

  26. Enard, W., Khaitovich, P., Klose, J., Zollner, S., Heissig, F., Giavalisco, P., Nieselt-Struwe, K., Muchmore, E., Varki, A., Ravid, R., Doxiadis, G.M., Bontrop, R.E., and Paabo, S., Science, 2002, vol. 296, pp. 340–343.

    Article  CAS  PubMed  Google Scholar 

  27. Buzdin, A., Ustyugova, S., Gogvadze, E., Lebedev, Y., Hunsmann, G., and Sverdlov, E., Hum. Genet., 2003, vol. 112, pp. 527–533.

    CAS  PubMed  Google Scholar 

  28. Wang, H., Xing, J., Grover, D., Hedges, D.J., Han, K., Walker, J.A., and Batzer, M.A., J. Mol. Biol., 2005, vol. 354, pp. 994–1007.

    Article  CAS  PubMed  Google Scholar 

  29. Sen, S.K., Han, K., Wang, J., Lee, J., Wang, H., Callinan, P.A., Dyer, M., Cordaux, R., Liang, P., and Batzer, M.A., Am. J. Hum. Genet., 2006, vol. 79, pp. 41–53.

    Article  CAS  PubMed  Google Scholar 

  30. Brosius, J., Gene, 1999, vol. 238, pp. 115–134.

    Article  CAS  PubMed  Google Scholar 

  31. Lebedev, Y.B., Amosova, A.L., Mamedov, I.Z., Fisunov, G.Y., and Sverdlov, E.D., Gene, 2007, vol. 390, pp. 122–129.

    Article  CAS  PubMed  Google Scholar 

  32. Buzdin, A., TheScientificWorld J., 2007, vol. 7, pp. 1848–1868.

    CAS  Google Scholar 

  33. Buzdin, A., Ustyugova, S., Khodosevich, K., Mamedov, I., Lebedev, Y., Hunsmann, G., and Sverdlov, E., Genomics, 2003, vol. 81, pp. 149–156.

    Article  CAS  PubMed  Google Scholar 

  34. Ruda, V.M., Akopov, S.B., Trubetskoy, D.O., Manuylov, N.L., Vetchinova, A.S., Zavalova, L.L., Nikolaev, L.G., and Sverdlov, E.D., Virus Res., 2004, vol. 104, pp. 11–16.

    Article  CAS  PubMed  Google Scholar 

  35. Sverdlov, E.D., BioEssays, 2000, vol. 22, pp. 161–171.

    Article  CAS  PubMed  Google Scholar 

  36. Kovalskaya, E., Buzdin, A., Gogvadze, E., Vinogradova, T., and Sverdlov, E., Virology, 2006, vol. 346, pp. 373–378.

    Article  CAS  PubMed  Google Scholar 

  37. Hughes, J.F. and Coffin, J.M., Proc. Natl. Acad. Sci. USA, 2004, vol. 101, pp. 1668–1672.

    Article  CAS  PubMed  Google Scholar 

  38. Ruprecht, K., Ferreira, H., Flockerzi, A., Wahl, S., Sauter, M., Mayer, J., and Mueller-Lantzsch, N., J. Virol., 2008, vol. 82, pp. 10008–10016.

    Article  CAS  PubMed  Google Scholar 

  39. Belshaw, R., Dawson, A.L., Woolven-Allen, J., Redding, J., Burt, A., and Tristem, M., J. Virol., 2005, vol. 79, pp. 12507–12514.

    Article  CAS  PubMed  Google Scholar 

  40. Medstrand, P. and Mager, D.L., J. Virol., 1998, vol. 72, pp. 9782–9787.

    CAS  PubMed  Google Scholar 

  41. Akopov, S.B., Nikolaev, L.G., Khil, P.P., Lebedev, Y.B., and Sverdlov, E.D., FEBS Lett., 1998, vol. 421, pp. 229–233.

    Article  CAS  PubMed  Google Scholar 

  42. Lavie, L., Kitova, M., Maldener, E., Meese, E., and Mayer, J., J. Virol., 2005, vol. 79, pp. 876–883.

    Article  CAS  PubMed  Google Scholar 

  43. Khodosevisc, K., Lebedev, Y., and Sverdlov, E., Bioorg. Khim., 2004, vol. 30, pp. 493–498 [Russ. J. Bioorg. Chem. (Engl. Transl.), 2004, vol. 30, pp. 441–445].

    Google Scholar 

  44. Vinogradova, T., Leppik, L., Kalinina, E., Zhulidov, P., Grzeschik, K.H., and Sverdlov, E., Mol. Genet. Genom., 2002, vol. 266, pp. 796–805.

    Article  CAS  Google Scholar 

  45. Macfarlane, C. and Simmonds, P., J. Mol. Evol., 2004, vol. 59, pp. 642–656.

    Article  CAS  PubMed  Google Scholar 

  46. Bannert, N. and Kurth, R., Proc. Natl. Acad. Sci. USA, 2004, vol. 101 S.2, pp. 14572–14579.

    Article  CAS  PubMed  Google Scholar 

  47. Herve, C.A., Lugli, E.B., Brand, A., Griffiths, D.J., and Venables, P.J., Clin. Exp. Immunol., 2002, vol. 128, pp. 75–82.

    Article  CAS  PubMed  Google Scholar 

  48. Boller, K., Konig, H., Sauter, M., Mueller-Lantzsch, N., Lower, R., Lower, J., and Kurth, R., Virology, 1993, vol. 196, pp. 349–353.

    Article  CAS  PubMed  Google Scholar 

  49. Andersson, A.C., Svensson, A.C., Rolny, C., Andersson, G., and Larsson, E., Int. J. Oncol., 1998, vol. 12, pp. 309–313.

    CAS  PubMed  Google Scholar 

  50. Hugin, A.W., Vacchio, M.S., and Morse, H.C., 3rd. Science, 1991, vol. 252, pp. 424–427.

    Article  CAS  PubMed  Google Scholar 

  51. Harris, J.M., McIntosh, E.M., and Muscat, G.E., Arch. Virol., 2000, vol. 145, pp. 353–363.

    Article  CAS  PubMed  Google Scholar 

  52. Contreras-Galindo, R., Contreras-Galindo, A., Lorenzo, E., and Yamamura, Y., Retrovirology, 2006, vol. 3,Suppl. 1, p. s33.

    Article  Google Scholar 

  53. Galli, U.M., Sauter, M., Lecher, B., Maurer, S., Herbst, H., Roemer, K., and Mueller-Lantzsch, N., Oncogene, 2005, vol. 24, pp. 3223–3228.

    Article  CAS  PubMed  Google Scholar 

  54. Denner, J., Persin, C., Vogel, T., Haustein, D., Norley, S., and Kurth, R., J. Acquir. Immune Defic. Syndr. Hum. Retrovirol., 1996, vol. 12, pp. 442–450.

    CAS  PubMed  Google Scholar 

  55. Melder, D.C., Pankratz, V.S., and Federspiel, M.J., J. Virol., 2003, vol. 77, pp. 10504–10514.

    Article  CAS  PubMed  Google Scholar 

  56. Best, S., Le Tissier P.R., Stoye J.P. Trends Microbiol., 1997, vol. 5, pp. 313–318.

    Article  CAS  PubMed  Google Scholar 

  57. Illarionova, A.E., Vinogradova, T.V., and Sverdlov, E.D., Virology, 2007, vol. 358, pp. 39–47.

    Article  CAS  PubMed  Google Scholar 

  58. Domansky, A.N., Kopantzev, E.P., Snezhkov, E.V., Lebedev, Y.B., Leib-Mosch, C., and Sverdlov, E.D., FEBS Lett., 2000, vol. 472, pp. 191–195.

    Article  CAS  PubMed  Google Scholar 

  59. Buzdin, A., Kovalskaya-Alexandrova, E., Gogvadze, E., and Sverdlov, E., Nucleic Acid Res., 2006, vol. 34, p. e67.

    Article  PubMed  Google Scholar 

  60. Buzdin, A., Kovalskaya-Alexandrova, E., Gogvadze, E., and Sverdlov, E., J. Virol., 2006, vol. 80, pp. 10752–10762.

    Article  CAS  PubMed  Google Scholar 

  61. Buzdin, A.A., Lebedev, Yu.V., and Sverdlov, E.D., Bioorg. Khim., 2003, vol. 29, pp. 103–106 [Russ. J. Bioorg. Chem. (Engl. Transl.), 2003, vol. 29, pp. 91–93].

    CAS  PubMed  Google Scholar 

  62. Gogvadze, E., Stukacheva, E., Buzdin, A., and Sverdlov, E., J. Virol., 2009 (in press).

  63. Aalkjaer, C., Frische, S., Leipziger, J., Nielsen, S., and Praetorius, J., Acta Physiol. Scand., 2004, vol. 181, pp. 505–512.

    Article  CAS  PubMed  Google Scholar 

  64. Rosenbaum, J.L. and Witman, G.B., Nat. Rev. Mol. Cell. Biol., 2002, vol. 3, pp. 813–825.

    Article  CAS  PubMed  Google Scholar 

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  1. Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, Moscow, 117997, Russia

    A. A. Buzdin

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Original Russian Text © A.A. Buzdin, 2010, published in Bioorganicheskaya Khimiya, 2010, Vol. 36, No. 1, pp. 38–46.

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Buzdin, A.A. A functional analysis of retroviral endogenous inserts in view of human genome evolution. Russ J Bioorg Chem 36, 32–39 (2010). https://doi.org/10.1134/S1068162010010048

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