Retrotransposons and their recognition of pol II promoters: A comprehensive survey of the transposable elements from the complete genome sequence of Schizosaccharomyces pombe

Genome Research

Volumn 13, Issue 9, 2003, Pages 1984-1997

  Bowen, Nathan J ^a,d   Jordan, I King ^b   Epstein, Jonathan A ^a   Wood, Valerie ^c   Levin, Henry L ^a  

^a EUNICE KENNEDY SHRIVER NATIONAL INSTITUTE OF CHILD HEALTH AND HUMAN DEVELOPMENT   (United States)

^b NATIONAL INSTITUTES OF HEALTH   (United States)

^c WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^d University of Georgia ^*  (United States)

Author keywords

[No Author keywords available]

Indexed keywords

NUCLEOTIDE; RNA POLYMERASE; TRANSFER RNA;

ARTICLE; CENTROMERE; CHROMOSOME ANALYSIS; CONTROLLED STUDY; DNA SEQUENCE; GENE CLUSTER; GENE INSERTION; GENE LOCATION; GENETIC CODE; GENETIC RECOMBINATION; GENOME ANALYSIS; LONG TERMINAL REPEAT; MOLECULAR EVOLUTION; MOLECULAR PHYLOGENY; MOLECULAR RECOGNITION; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROMOTER REGION; RETROPOSON; SCHIZOSACCHAROMYCES POMBE; SEQUENCE HOMOLOGY; STRAIN DIFFERENCE; TANDEM REPEAT; TRANSPOSON;

CHROMOSOME MAPPING; CHROMOSOMES, FUNGAL; COMPUTATIONAL BIOLOGY; DNA POLYMERASE II; EVOLUTION, MOLECULAR; GENOME, FUNGAL; MUTAGENESIS, INSERTIONAL; PHYLOGENY; PROMOTER REGIONS (GENETICS); RECOMBINATION, GENETIC; RETROELEMENTS; SCHIZOSACCHAROMYCES; TERMINAL REPEAT SEQUENCES;

FUNGI; INSERTION SEQUENCES; MYXOGASTRIA; SCHIZOSACCHAROMYCES; SCHIZOSACCHAROMYCES POMBE; TRANSPOSONS;

EID: 0141630486     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.1191603     Document Type: Article

References (53)

1. Ahmad, K. and Henikoff, S. 2002. The histone variant H3.3 marks active chromatin by replication-independent nucleosome assembly. Mol. Cell 9: 1191-1200.
2. Behrens, R., Hayles, J., and Nurse, P. 2000. Fission yeast retrotransposon Tf1 integration is targeted to 5′ ends of open reading frames. Nucleic Acids Res. 28: 4709-4716.
3. Berbee, M. L. and Taylor, J.W. 1993. Dating the evolutionary radiations of the true fungi. Canadian J. Botany-Revue Canadienne De Botanique 718: 1114-1127.
4. Boeke, J.D. and Stoye, J.P. 1997. Retrotransposons, endogenous retroviruses, and the evolution of retroelements. In Retroviruses (eds. J.M. Coffin et al.), pp. 343-436. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
5. Bowen, N.J. and McDonald, J.F. 1999. Genomic analysis of Caenorhabditis elegans reveals ancient families of retroviral-like elements. Genome Res. 9: 924-935.
6. Bowen, N.J. and McDonald, J.F. 2001. Drosophila euchromatic LTR retrotransposons are much younger than the host species in which they reside. Genome Res. 119: 1527-1540.
7. Britten, R.J. 1998. Precise sequence complementarity between yeast chromosome ends and two classes of just-subtelomeric sequences. Proc. Natl. Acad. Sci. 95: 5906-5912.
8. Bryk, M., Banerjee, M., Conte Jr., D., and Curcio, M.J. 2001. The Sgs1 helicase of Saccharomyces cerevisiae inhibits retrotransposition of Ty1 multimeric arrays. Mol. Cell Biol 21: 5374-5388.
9. Chalker, D.L. and Sandmeyer, S.B. 1992. Ty3 integrates within the region of RNA polymerase III transcription initiation. Genes & Dev. 6: 117-128.
10. Coffin, J.M., Hughes, S.H., and Varmus, H.E. eds. 1997. Retroviruses. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
11. Costas, J. and Naveira, H. 2000. Evolutionary history of the human endogenous retrovirus family ERV9. Mol. Biol. Evol. 17: 320-330.
12. Csink, A.K. and McDonald, J.F. 1995. Analysis of copia sequence variation within and between Drosophila species. Mol. Biol. Evol. 12: 83-93.
13. Ganko, E.W., Fielman, K.T., and McDonald, J.F. 2001. Evolutionary history of Cer elements and their impact on the C. elegans genome. Genome Res. 11: 2066-2074.
14. Genetics Computer Group, 1999. Wisconsin Package Version 10.0. Madison, WI.
15. Goodwin, T.J. and Poulter, R.T. 2000. Multiple LTR-retrotransposon families in the asexual yeast Candida albicans. Genome Res. 10: 174-191.
16. Grewal, S.I. and Elgin, S.C. 2002. Heterochromatin: new possibilities for the inheritance of structure. Curr. Opin. Genet. Dev. 12: 178-187.
17. Hoff, E.F., Levin, H.L., and Boeke, J.D. 1998. Schizosaccharomyces pombe retrotransposon Tf2 mobilizes primarily through homologous cDNA recombination. Mol. Cell Biol 18: 6839-6852.
18. Jordan, I.K. and McDonald, J.F. 1999. Tempo and mode of Ty element evolution in Saccharomyces cerevisiae. Genetics 151: 1341-1351.
19. Kapitonov, V. and Jurka, J. 1996. The age of Alu subfamilies. J. Mol. Evol. 42: 59-65.
20. Kim, J.M., Vanguri, S., Boeke, J.D., Gabriel, A., and Voytas, D.F. 1998. Transposable elements and genome organization: A comprehensive survey of retrotransposons revealed by the complete Saccharomyces cerevisiae genome sequence. Genome Res. 8: 464-478.
21. Kumar, S., Tamura, K., Jakobsen, I.B., and Nei, M. 2001. MEGA2: Molecular evolutionary genetics analysis software. Bioinformatics 1712: 1244-1245.
22. 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.
23. Lespinet, O., Wolf, Y.I., Koonin, E.V., and Aravind, L. 2002. The role of lineage-specific gene family expansion in the evolution of eukaryotes. Genome Res. 12: 1048-1059.
24. Levin, H.L. 1995. A novel mechanism of self-primed reverse transcription defines a new family of retroelements. Mol. Cell. Biol. 15: 3310-3317.
25. Levin, H.L. 1996. An unusual mechanism of self-primed reverse transcription requires the RNase H domain of reverse transcriptase to cleave an RNA duplex. Mol. Cell Biol. 16: 5645-5654.
26. Levin, H.L. and Boeke, J.D. 1992. Demonstration of retrotransposition of the Tf1 element in fission yeast. EMBO J. 11: 1145-1153.
27. Levin, H.L., Weaver, D.C. and Boeke, J.D. 1990. Two related families of retrotransposons from Schizosaccharomyces pombe. Mol. Cell Biol. 10: 6791-6798.
28. Lipman, D.J., Wilbur, W.J., Smith, T.F., and Waterman, M.S. 1984. On the statistical significance of nucleic acid similarities. Nucleic Acids Res. 12: 215-226.
29. Malik, H.S. and Eickbush, T.H. 1999. Modular evolution of the integrase domain in the Ty3/Gypsy class of LTR retrotransposons. J. Virol. 73: 5186-5190.
30. Mata, J., Lyne, R., Burns, G., and Bahler, J. 2002. The transcriptional program of meiosis and sporulation in fission yeast. Nat. Genet. 32: 143-147.
31. Medstrand, P., van de Lagemaat, L.N., and Mager, D.L. 2002. Retroelement distributions in the human genome: Variations associated with age and proximity to genes. Genome Res. 12: 1483-1495.
32. Roeder, G.S. and Fink, G.R. 1983. Transposable elements in yeast, pp. 299-326. Academic Press, New York.
33. Rutherford, K., Parkhill, J., Crook, J., Horsnell, T., Rice, P., Rajandream, M.A., and Barrell, B. 2000. Artemis: Sequence visualization and annotation. Bioinformatics 16: 944-945.
34. SanMiguel, P., Tikhonov, A., Jin, Y.K., Motchoulskaia, N., Zakharov, D., Melake-Berhan, A., Springer, P.S., Edwards, K.J., Lee, M., Avramova, Z. et al. 1996. Nested retrotransposons in the intergenic regions of the maize genome. Science 274: 765-768.
35. Scherthan, H., Bahler, J. and Kohli, J. 1994. Dynamics of chromosome organization and pairing during meiotic prophase in fission yeast. J. Cell Biol. 127: 273-285.
36. Schroder, A.R., Shinn, P., Chen, H., Berry, C., Ecker, J.R., and Bushman, F. 2002. HIV-1 integration in the human genome favors active genes and local hotspots. Cell 110: 521-529.
37. Schuler, G.D., Altschul, S.F., and Lipman, D.J. 1991. A workbench for multiple alignment construction and analysis. Proteins 9: 180-190.
38. Singleton, T.L. and Levin, H.L. 2002. A long terminal repeat retrotransposon of fission yeast has strong preferences for specific sites of insertion. Eukaryotic Cell 1: 44-55.
39. Sipiczki, M. 2000. Where does fission yeast sit on the tree of life? Genome Biol. 1: REVIEWS1011.
40. Stajich, J.E., Block, D., Boulez, K., Brenner, S.E., Chervitz, S.A., Dagdigian, C., Fuellen, G., Gilbert, J.G.R., Korf, I., Lapp, H., et al. 2002. The Bioperl toolkit: Perl modules for the life sciences. Genome Res. 12: 1611-1618.
41. Teysset, L., Dang, V.D., Kim, M.K., and Levin, H.L. 2003. A long terminal repeat-containing retrotransposon of Schizosaccharomyces pombe expresses a Gag-like protein that assembles into virus-like particles which mediate reverse transcription. J. Virol. 77: 5451-5463.
42. Thompson, J.D., Gibson, T.J., Plewniak, F., Jeanmougin, F., and Higgins, D.G. 1997. The CLUSTALwindows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25: 4876-4882.
43. Uzun, O. and Gabriel, A. 2001. A Ty1 reverse transcriptase active-site aspartate mutation blocks transposition but not polymerization. J. Virol. 75: 6337-6347.
44. Watanabe, T., Miyashita, K., Saito, T.T., Yoneki, T., Kakihara, Y., Nabeshima, K., Kishi, Y.A., Shimoda, C., and Nojima, H. 2001. Comprehensive isolation of meiosis-specific genes identifies novel proteins and unusual non-coding transcripts in Schizosaccharomyces pombe. Nucleic Acids Res. 29: 2327-2337.
45. Weidhaas, J.B., Angelichio, E.L., Fenner, S., and Coffin, J.M. 2000. Relationship between retroviral DNA integration and gene expression. J. Virol. 74: 8382-8389.
46. Withers-Ward, E.S., Kitamura, Y., Barnes, J.P., and Coffin, J.M. 1994. Distribution of targets for avian retrovirus DNA integration in vivo. Genes & Dev. 8: 1473-1487.
47. Wood, V., Gwilliam, R., Rajandream, M.A., Lyne, M., Lyne, R., Stewart, A., Sgouros, J., Peat, N., Hayles, J., Baker, S., et al. 2002. The genome sequence of Schizosaccharomyces pombe. Nature 415: 871-880.
48. Xie, W., Gai, X., Zhu, Y., Zappulla, D.C., Sternglanz, R., and Voytas, D.F. 2001. Targeting of the yeast Ty5 retrotransposon to silent chromatin is mediated by interactions between integrase and Sir4p. Mol. Cell Biol. 21: 6606-6614.
49. Xiong, Y. and Eickbush, T.H. 1988. Similarity of reverse transcriptase-like sequences of viruses, transposable elements, and mitochondrial introns. Mol. Biol. Evol. 5: 675-690.
50. Xiong, Y. and Eickbush, T.H. 1990. Origin and evolution of retroelements based upon their reverse transcriptase sequences. EMBO J. 9: 3353-3362.
51. Yieh, L., Kassavetis, G., Geiduschek, E.P., and Sandmeyer, S.B. 2000. The Brf and TATA-binding protein subunits of the RNA polymerase III transcription factor IIIB mediate position-specific integration of the gypsy-like element, Ty3. J. Biol. Chem. 275: 29800-29807.
52. Zou, S. and Voytas, D.F. 1997. Silent chromatin determines target preference of the Saccharomyces retrotransposon Ty5. Proc. Natl. Acad. Sci. 94: 7412-7416.
53. Zou, S., Ke, N., Kim, J.M., and D.F. Voytas. 1996. The Saccharomyces retrotransposon Ty5 integrates preferentially into regions of silent chromatin at the telomeres and mating loci. Genes & Dev. 10: 634-645.