Large-scale discovery of insertion hotspots and preferential integration sites of human transposed elements

Nucleic Acids Research

Volumn 38, Issue 5, 2009, Pages 1515-1530

  Levy, Asaf ^a   Schwartz, Schraga ^a   Ast, Gil ^a  

^a TEL AVIV UNIVERSITY   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; PROTEIN ALU; PROTEIN ERV1; PROTEIN HAT; PROTEIN MALR; REGULATOR PROTEIN; UNCLASSIFIED DRUG;

ARTICLE; CONSENSUS SEQUENCE; CONTROLLED STUDY; DNA INTEGRATION; DNA TRANSPOSITION; GENE INSERTION SEQUENCE; GENE TARGETING; GENETIC CONSERVATION; HUMAN; HUMAN GENOME; MOLECULAR MECHANICS; PRIORITY JOURNAL; PROTEIN FAMILY; PROTEIN MOTIF; RETROPOSON; TRANSPOSON; ALU SEQUENCE; BIOLOGICAL MODEL; CHEMISTRY; GENOMICS; INTERSPERSED REPEAT; METHODOLOGY; MOLECULAR EVOLUTION; NUCLEOTIDE SEQUENCE;

EUKARYOTA;

ALU ELEMENTS; BASE SEQUENCE; DNA; EVOLUTION, MOLECULAR; GENOME, HUMAN; GENOMICS; HUMANS; INTERSPERSED REPETITIVE SEQUENCES; MODELS, GENETIC;

EID: 77950473787     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkp1134     Document Type: Article

References (52)

1. Aparicio, S., Chapman, J., Stupka, E., Putnam, N., Chia, J.M., Dehal, P., Christoffels, A., Rash, S., Hoon, S., Smit, A. et al. (2002) Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Science, 297, 1301-1310.
2. Biemont, C. and Vieira, C. (2006) Genetics: junk DNA as an evolutionary force. Nature, 443, 521-524.
3. Consortium, I.C.G.S. (2004) Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature, 432, 695-716.
4. Lander, E.S., Linton, L.M., Birren, B., Nusbaum, C., Zody, M.C., Baldwin, J., Devon, K., Dewar, K., Doyle, M., FitzHugh, W. et al. (2001) Initial sequencing and analysis of the human genome. Nature, 409, 860-921.
5. Waterston, R.H., Lindblad-Toh, K., Birney, E., Rogers, J., Abril, J.F., Agarwal, P., Agarwala, R., Ainscough, R., Alexandersson, M., An, P. et al. (2002) Initial sequencing and comparative analysis of the mouse genome. Nature, 420, 520-562.
6. Hedges, D.J. and Batzer, M.A. (2005) From the margins of the genome: mobile elements shape primate evolution. Bioessays, 27, 785-794.
7. Goodier, J.L. and Kazazian, H.H. Jr (2008) Retrotransposons revisited: the restraint and rehabilitation of parasites. Cell, 135, 23-35.
8. Callinan, P.A. and Batzer, M.A. (2006) Retrotransposable elements and human disease. Genome Dyn., 1, 104-115.
9. Asch, H.L., Eliacin, E., Fanning, T.G., Connolly, J.L., Bratthauer, G. and Asch, B.B. (1996) Comparative expression of the LINE-1 p40 protein in human breast carcinomas and normal breast tissues. Oncol. Res., 8, 239-247.
10. Depil, S., Roche, C., Dussart, P. and Prin, L. (2002) Expression of a human endogenous retrovirus, HERV-K, in the blood cells of leukemia patients. Leukemia, 16, 254-259.
11. Muster, T., Waltenberger, A., Grassauer, A., Hirschl, S., Caucig, P., Romirer, I., Fodinger, D., Seppele, H., Schanab, O., Magin-Lachmann, C. et al. (2003) An endogenous retrovirus derived from human melanoma cells. Cancer Res., 63, 8735-8741.
12. Ast, G. (2004) How did alternative splicing evolve? Nat. Rev. Genet., 5, 773-782.
13. Corvelo, A. and Eyras, E. (2008) Exon creation and establishment in human genes. Genome Biol., 9, R141.
14. Kim, E., Goren, A. and Ast, G. (2008) Alternative splicing: current perspectives. Bioessays, 30, 38-47.
15. VolffJ, N. and Brosius, J. (2007) Modern genomes with retro-look: retrotransposed elements, retroposition and the origin of new genes. Genome Dyn., 3, 175-190.
16. Barbosa-Morais, N.L., Carmo-Fonseca, M. and Aparicio, S. (2006) Systematic genome-wide annotation of spliceosomal proteins reveals differential gene family expansion. Genome Res., 16, 66-77.
17. Sela, N., Mersch, B., Gal-Mark, N., Lev-Maor, G., Hotz-Wagenblatt, A. and Ast, G. (2007) Comparative analysis of transposed element insertion within human and mouse genomes reveals Alu's unique role in shaping the human transcriptome. Genome Biol., 8, R127.
18. Conley, A.B., Miller, W.J. and Jordan, I.K. (2008) Human cis natural antisense transcripts initiated by transposable elements. Trends Genet., 24, 53-56.
19. Conley, A.B., Piriyapongsa, J. and Jordan, I.K. (2008) Retroviral promoters in the human genome. Bioinformatics, 24, 1563-1567.
20. Jordan, I.K., Rogozin, I.B., Glazko, G.V. and Koonin, E.V. (2003) Origin of a substantial fraction of human regulatory sequences from transposable elements. Trends Genet., 19, 68-72.
21. Piriyapongsa, J. and Jordan, I.K. (2007) A family of human microRNA genes from miniature inverted-repeat transposable elements. PLoS ONE, 2, e203.
22. Piriyapongsa, J., Marino-Ramirez, L. and Jordan, I.K. (2007) Origin and evolution of human microRNAs from transposable elements. Genetics, 176, 1323-1337.
23. Giordano, J., Ge, Y., Gelfand, Y., Abrusan, G., Benson, G. and Warburton, P. (2007) Evolutionary history of mammalian transposons determined by genome-wide defragmentation. PLoS Comput. Biol., 3, e137.
24. Pace, J.K. II and Feschotte, C. (2007) The evolutionary history of human DNA transposons: evidence for intense activity in the primate lineage. Genome Res., 17, 422-432.
25. Abrusan, G., Giordano, J. and Warburton, P.E. (2008) Analysis of transposon interruptions suggests selection for L1 elements on the X chromosome. PLoS Genet., 4, e1000172.
26. Ichiyanagi, K., Nakajima, R., Kajikawa, M. and Okada, N. (2007) Novel retrotransposon analysis reveals multiple mobility pathways dictated by hosts. Genome Res., 17, 33-41.
27. Bergman, C.M., Quesneville, H., Anxolabehere, D. and Ashburner, M. (2006) Recurrent insertion and duplication generate networks of transposable element sequences in the Drosophila melanogaster genome. Genome Biol., 7, R112.
28. Kriegs, J.O., Matzke, A., Churakov, G., Kuritzin, A., Mayr, G., Brosius, J. and Schmitz, J. (2007) Waves of genomic hitchhikers shed light on the evolution of gamebirds (Aves: Galliformes). BMC Evol. Biol., 7, 190.
29. Karolchik, D., Hinrichs, A.S., Furey, T.S., Roskin, K.M., Sugnet, C.W., Haussler, D. and Kent, W.J. (2004) The UCSC Table Browser data retrieval tool. Nucleic Acids Res., 32, D493-496.
30. Benjamini, Y. and Hochberg, Y. (1995) Controlling the false discovery rate-a practical and powerful approach to multiple testing. J. Roy. Stat. Soc., 57, 289-300.
31. Grimaldi, G., Skowronski, J. and Singer, M.F. (1984) Defining the beginning and end of KpnI family segments. EMBO J., 3, 1753-1759.
32. Giardine, B., Riemer, C., Hardison, R.C., Burhans, R., Elnitski, L., Shah, P., Zhang, Y., Blankenberg, D., Albert, I., Taylor, J. et al. (2005) Galaxy: a platform for interactive large-scale genome analysis. Genome Res., 15, 1451-1455.
33. Bembom, O. (2007) seqLogo: An R package for plotting DNA sequence logos.
34. Gibbs, R.A., Rogers, J., Katze, M.G., Bumgarner, R., Weinstock, G.M., Mardis, E.R., Remington, K.A., Strausberg, R.L., Venter, J.C., Wilson, R.K. et al. (2007) Evolutionary and biomedical insights from the rhesus macaque genome. Science, 316, 222-234.
35. Csárdi, G. and Nepusz, T. (2006) The igraph software package for complex network research. InterJournal, Complex Systems, 1696.
36. Wicker, T., Sabot, F., Hua-Van, A., Bennetzen, J.L., Capy, P., Chalhoub, B., Flavell, A., Leroy, P., Morgante, M., Panaud, O. et al. (2007) A unified classification system for eukaryotic transposable elements. Nat. Rev. Genet., 8, 973-982.
37. Kempken, F. and Windhofer, F. (2001) The hAT family: a versatile transposon group common to plants, fungi, animals, and man. Chromosoma, 110, 1-9.
38. Smit, A.F. and Riggs, A.D. (1996) Tiggers and DNA transposon fossils in the human genome. Proc. Natl Acad. Sci. USA, 93, 1443-1448.
39. Jurka, J. (1997) Sequence patterns indicate an enzymatic involvement in integration of mammalian retroposons. Proc. Natl Acad. Sci. USA, 94, 1872-1877.
40. Khan, H., Smit, A. and Boissinot, S. (2006) Molecular evolution and tempo of amplification of human LINE-1 retrotransposons since the origin of primates. Genome Res., 16, 78-87.
41. Sironi, M., Menozzi, G., Comi, G.P., Cereda, M., Cagliani, R., Bresolin, N. and Pozzoli, U. (2006) Gene function and expression level influence the insertion/fixation dynamics of distinct transposon families in mammalian introns. Genome Biol., 7, R120.
42. Simons, C., Pheasant, M., Makunin, I.V. and Mattick, J.S. (2006) Transposon-free regions in mammalian genomes. Genome Res., 16, 164-172.
43. van de Lagemaat, L.N., Medstrand, P. and Mager, D.L. (2006) Multiple effects govern endogenous retrovirus survival patterns in human gene introns. Genome Biol., 7, R86.
44. Stenger, J.E., Lobachev, K.S., Gordenin, D., Darden, T.A., Jurka, J. and Resnick, M.A. (2001) Biased distribution of inverted and direct Alus in the human genome: implications for insertion, exclusion, and genome stability. Genome Res., 11, 12-27.
45. Schmitz, J., Churakov, G., Zischler, H. and Brosius, J. (2004) A novel class of mammalian-specific tailless retropseudogenes. Genome Res., 14, 1911-1915.
46. Luan, D.D., Korman, M.H., Jakubczak, J.L. and Eickbush, T.H. (1993) Reverse transcription of R2Bm RNA is primed by a nick at the chromosomal target site: a mechanism for non-LTR retrotransposition. Cell, 72, 595-605.
47. Mandal, P.K. and Kazazian, H.H. Jr (2008) SnapShot: vertebrate transposons. Cell, 135, 191-192.e1.
48. Symer, D.E., Connelly, C., Szak, S.T., Caputo, E.M., Cost, G.J., Parmigiani, G. and Boeke, J.D. (2002) Human L1 retrotransposition is associated with genetic instability in vivo. Cell, 110, 327-338.
49. Siepel, A., Bejerano, G., Pedersen, J.S., Hinrichs, A.S., Hou, M., Rosenbloom, K., Clawson, H., Spieth, J., Hillier, L.W., Richards, S. et al. (2005) Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res., 15, 1034-1050.
50. Kondo, Y. and Issa, J.P. (2003) Enrichment for histone H3 lysine 9 methylation at Alu repeats in human cells. J. Biol. Chem., 278, 27658-27662.
51. Lowe, C.B., Bejerano, G. and Haussler, D. (2007) Thousands of human mobile element fragments undergo strong purifying selection near developmental genes. Proc. Natl Acad. Sci. USA, 104, 8005-8010.
52. Jurka, J. (2000) Repbase update: a database and an electronic journal of repetitive elements. Trends Genet., 16, 418-420.