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A new polymorphic retroelement database (PRED) for the human genome

  • Mathematical and System Biology
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Abstract

Comparison of primate genomic sequences has demonstrated that the intra-and interspecific genetic variation is provided by retroelements (REs). The human genome contains many thousands of polymorphic RE copies, which are regarded as a promising source of new generation molecular genetic markers. However, the absence of systematized data on the RE number, distribution, genomic context, and abundance in various human populations limits the use of RE insertion polymorphism. We designed the first bilingual (Russian/English) web resource on the known polymorphic REs discovered both by our team and other researchers. The database contains the information about the genomic location of each RE, its position relative to known and predicted genes, abundance in human populations, and other data. Our web portal (http://labcfg.ibch.ru/home.html) allows a search of the database with user-specified parameters. The database makes it possible to most comprehensively analyze the RE distribution in the human genome and to design molecular genetic markers for studies of human genome diversity and biomedical applications.

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References

  1. Caenorhabditis elegans Sequencing Consortium. 1998. Genome sequence of the nematode C. elegans: A platform for investigating biology. Science. 282, 2012–2018.

    Article  Google Scholar 

  2. Adams M.D., Celniker S.E., Holt R.A., et al. 2000. The genome sequence of Drosophila melanogaster. Science. 287, 2185–2195.

    Article  PubMed  Google Scholar 

  3. Aparicio J., Chapman E., Stupka N., et al. 2002. Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Science. 297, 1301–1310.

    Article  PubMed  CAS  Google Scholar 

  4. Human Genome Sequencing Consortium. 2001. Initial sequencing and analysis of the human genome. Nature. 409, 860–921.

    Article  Google Scholar 

  5. Mouse Genome Sequencing Consortium. 2002. Initial sequencing and comparative analysis of the mouse genome. Nature. 420, 520–562.

    Article  CAS  Google Scholar 

  6. Jurka J., Kapitonov V.V., Kohany O., Jurka M.V. 2007. Repetitive sequences in complex genomes: Structure and evolution. Annu. Rev. Gen. Hum. Genet. 8, 241–259.

    Article  CAS  Google Scholar 

  7. Mills R.E., Bennett E.A., Iskow R.C., Devine S.E. 2007. Which transposable elements are active in the human genome? Trends Genet. 23, 183–191.

    Article  PubMed  CAS  Google Scholar 

  8. Bowen N.J., Jordan I.K. 2002. Transposable elements and the evolution of eukaryotic complexity. Curr. Issues Mol. Biol. 4, 65–76.

    PubMed  CAS  Google Scholar 

  9. Deininger P.L., Moran J.V., Batzer M.A., Kazazian H.H., Jr. 2003. Mobile elements and mammalian genome evolution. Curr. Opin. Genet. Dev. 13, 651–658.

    Article  PubMed  CAS  Google Scholar 

  10. Lebedev Y.B., Amosova A.L., Mamedov I.Z., Fisunov G.Y., Sverdlov E.D. 2007. Most recent AluY insertions in human gene introns reduce the content of the primary transcripts in a cell type specific manner. Gene. 390, 122–129.

    Article  PubMed  CAS  Google Scholar 

  11. Ustiugova S.V., Amosova A.L., Lebedev Iu.B., Sverdlov E.D. 2006. A tissue-specific decrease in the pre-mRNA level of L1-and Alu-containing alleles of human genes. Bioorg. Khim. 32, 103–106.

    PubMed  CAS  Google Scholar 

  12. Lebedev Y.B., Belonovitch O.S., Zybrova N.V., Khil P.P., Kurdyukov S.G., Vinogradova T.V., Hunsmann G., Sverdlov E.D. 2000. Differences in HERV-K LTR insertions in orthologous loci of humans and great apes. Gene. 247, 265–277.

    Article  PubMed  CAS  Google Scholar 

  13. Mamedov I., Batrak A., Buzdin A., Arzumanyan E., Lebedev Y., Sverdlov E.D. 2002. Genome-wide comparison of differences in the integration sites of interspersed repeats between closely related genomes. Nucleic Acids Res. 30, e71.

    Article  PubMed  Google Scholar 

  14. Mamedov I., Lebedev Y., Hunsmann G., Khusnutdinova E., Sverdlov E. 2004. A rare event of insertion polymorphism of a HERV-K LTR in the human genome. Genomics. 84, 596–599.

    Article  PubMed  CAS  Google Scholar 

  15. Buzdin A., Ustyugova S., Khodosevich K., Mamedov I., Lebedev Y., Hunsmann G., Sverdlov E. 2003. Human-specific subfamilies of HERV-K (HML-2) long terminal repeats: Three master genes were active simultaneously during branching of hominoid lineages. Genomics. 81, 149–156.

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  17. Price A.L., Eskin E., Pevzner P.A. 2004. Whole-genome analysis of Alu repeat elements reveals complex evolutionary history. Genome Res. 14, 2245–2252.

    Article  PubMed  CAS  Google Scholar 

  18. Mamedov I.Z., Arzumanyan E.S., Amosova A.L., Lebedev Y.B., Sverdlov E.D. 2005. Whole-genome experimental identification of insertion/deletion polymorphisms of interspersed repeats by a new general approach. Nucleic Acids Res. 33, e16.

    Article  PubMed  CAS  Google Scholar 

  19. Boissinot S., Chevret P., Furano A.V. 2000. L1 (LINE-1) retrotransposon evolution and amplification in recent human history. Mol. Biol. Evol. 17. 915–928.

    PubMed  CAS  Google Scholar 

  20. Carter A.B., Salem A.-H., Hedges D.J., Nguyen Keegan C., Kimball B., Walker J.A., Watkins W.S., Jorde L.B., Batzer M.A. 2004. Genome wide analysis of the human Alu Yb lineage. Human Genomics. 1. 167–178.

    PubMed  CAS  Google Scholar 

  21. Otieno A.C., Carter A.B., Hedges D.J., et al. 2004. Analysis of the human Alu Ya-lineage. J. Mol. Biol. 342, 109–118.

    Article  PubMed  CAS  Google Scholar 

  22. Konkel M.K., Wang J., Liang P., Batzer M.A. 2007. Identification and characterization of novel polymorphic LINE-1 insertions through comparison of two human genome sequence assemblies. Gene. 390, 28–38.

    Article  PubMed  CAS  Google Scholar 

  23. Myers J.S., Vincent B.J., Udall H., et al. 2002. A comprehensive analysis of recently integrated human Ta L1 elements. Am. J. Hum. Genet. 71. 312–326.

    Article  PubMed  CAS  Google Scholar 

  24. Antunez-de-Mayolo G., Antunez-de-Mayolo A., Antunez-de-Mayolo P., et al. 2002. Phylogenetics of worldwide human populations as determined by polymorphic Alu insertions. Electrophoresis. 23, 3346–3356.

    Article  PubMed  CAS  Google Scholar 

  25. Dornelles C.L., Battilana J., Fagundes N.J., Freitas L.B., Bonatto S.L., Salzano F.M. 2004. Mitochondrial DNA and Alu insertions in a genetically peculiar population: The Ayoreo Indians of Bolivia and Paraguay. Am. J. Hum. Biol. 16, 479–488.

    Article  PubMed  CAS  Google Scholar 

  26. Nasidze I., Risch G.M., Robichaux M., Sherry S.T., Batzer M.A., Stoneking M. 2001. Alu insertion polymorphisms and the genetic structure of human populations from the Caucasus. Eur. J. Hum. Genet. 9, 267–272.

    Article  PubMed  CAS  Google Scholar 

  27. Ustyugova S.V., Amosova A.L., Lebedev Y.B., Sverdlov E.D. 2005. Cell line fingerprinting using retroelement insertion polymorphism. Biotechniques. 38, 561–565.

    Article  PubMed  CAS  Google Scholar 

  28. Rajeevan H., Osier M.V., Cheung K.H., et al. 2003. ALFRED: The ALelle FREquency Database. Update. Nucleic Acids Res. 31, 270–271.

    Article  PubMed  CAS  Google Scholar 

  29. Paces J., Pavlicek A., Paces V. 2002. HERVd: Database of human endogenous retroviruses. Nucleic Acids Res. 30, 205–206.

    Article  PubMed  CAS  Google Scholar 

  30. Buzdin A., Gogvadze E., Kovalskaya E., et al. 2003. The human genome contains many types of chimeric retro-genes generated through in vivo RNA recombination. Nucleic Acids Res. 31, 4385–4390.

    Article  PubMed  CAS  Google Scholar 

  31. Buzdin A., Ustyugova S., Gogvadze E., Lebedev Y., Hunsmann G., Sverdlov E. 2003. Genome-wide targeted search for human specific and polymorphic L1 integrations. Hum. Genet. 112, 527–533.

    PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  33. Smit A.F., Toth G., Riggs A.D., Jurka J. 1995. Ancestral, mammalian-wide subfamilies of LINE-1 repetitive sequences. J. Mol. Biol. 246, 401–417.

    Article  PubMed  CAS  Google Scholar 

  34. Wang J., Song L., Gonder M.K., Azrak S., Ray D.A., Batzer M.A., Tishkoff S.A., Liang P. 2006. Whole genome computational comparative genomics: A fruitful approach for ascertaining Alu insertion polymorphisms. Gene. 365, 11–20.

    Article  PubMed  CAS  Google Scholar 

  35. Carroll M.L., Roy-Engel A.M., Nguyen S.V., et al. 2001. Large-scale analysis of the Alu Ya5 and Yb8 subfamilies and their contribution to human genomic diversity. J. Mol. Biol. 311, 17–40.

    Article  PubMed  CAS  Google Scholar 

  36. Salem A.H., Myers J.S., Otieno A.C., Watkins W.S., Jorde L.B., Batzer M.A. 2003. LINE-1 preTa elements in the human genome. J. Mol. Biol. 326, 1127–1146.

    Article  PubMed  CAS  Google Scholar 

  37. Hughes J.F., Coffin J.M. 2004. Human endogenous retrovirus K solo-LTR formation and insertional polymorphisms: Implications for human and viral evolution. Proc. Natl. Acad. Sci. USA. 101, 1668–1672.

    Article  PubMed  CAS  Google Scholar 

  38. Gabriel A., Dapprich J., Kunkel M., Gresham D., Pratt S.C., Dunham M.J. 2006. Global mapping of transposon location. PLoS Genet. 2, e212.

    Article  PubMed  CAS  Google Scholar 

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Authors and Affiliations

  1. Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia

    I. Z. Mamedov, A. L. Amosova, G. Yu. Fisunov & Yu. B. Lebedev

Authors
  1. I. Z. Mamedov
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  2. A. L. Amosova
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  3. G. Yu. Fisunov
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  4. Yu. B. Lebedev
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Corresponding author

Correspondence to I. Z. Mamedov.

Additional information

Original Russian Text © I.Z. Mamedov, A.L. Amosova, G.Yu. Fisunov, Yu.B. Lebedev, 2008, published in Molekulyarnaya Biologiya, 2008, Vol. 42, No. 4, pp. 721–727.

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Mamedov, I.Z., Amosova, A.L., Fisunov, G.Y. et al. A new polymorphic retroelement database (PRED) for the human genome. Mol Biol 42, 641–646 (2008). https://doi.org/10.1134/S0026893308040213

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  • DOI: https://doi.org/10.1134/S0026893308040213

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