Genome evolution mediated by Ty elements in Saccharomyces

Cytogenetic and Genome Research

Volumn 110, Issue 1-4, 2005, Pages 63-69

  Garfinkel, D J ^a  

^a NATIONAL CANCER INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA SEQUENCE; EUKARYOTE; FUNGAL GENETICS; GENE INSERTION; GENE REARRANGEMENT; GENETIC RECOMBINATION; LONG TERMINAL REPEAT; MOLECULAR EVOLUTION; MULTIGENE FAMILY; NONHUMAN; PRIORITY JOURNAL; RETROPOSON; REVIEW; SACCHAROMYCES;

ANIMALS; EVOLUTION, MOLECULAR; GENOME, FUNGAL; MAMMALS; MODELS, GENETIC; PLANTS; RETROELEMENTS; SACCHAROMYCES CEREVISIAE; TERMINAL REPEAT SEQUENCES;

EUKARYOTA; SACCHAROMYCES; SACCHAROMYCES CEREVISIAE;

EID: 18844460576     PISSN: 14248581     EISSN: None     Source Type: Journal    
DOI: 10.1159/000084939     Document Type: Review

References (62)

1. Albertson DG, Collins C, McCormick F, Gray JW: Chromosome aberrations in solid tumors. Nat Genet 34:369-376 (2003).
2. Boeke JD: Transposable elements in Saccharomyces cerevisiae, in Howe MM (ed): Mobile DNA, pp 335-374 (ASM Press, Washington DC 1989).
3. Boeke JD, Devine SE: Yeast retrotransposons: finding a nice quiet neighborhood. Cell 93:1087-1089 (1998).
4. Bolton EC, Boeke JD: Transcriptional interactions between yeast tRNA genes, Hanking genes and Ty elements: a genomic point of view. Genome Res 13:254-263 (2003).
5. Cliften P, Sudarsanam P, Desikan A, Fulton L, Fulton B, Majors J, Waterston R, Cohen BA, Johnston M: Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301:71-76 (2003).
6. Codon AC, Benitez T, Korhola M: Chromosomal reorganization during meiosis of Saccharomyces cerevisiae baker's yeasts. Curr Genet 32:247-259 (1997).
7. Craig NL, Craigie R, Gellert M, Lambowitz AM (eds): Mobile DNA II, pp 1-1204 (ASM Press, Washington DC 2002).
8. Curcio MJ, Garfinkel DJ: Single-step selection for Ty1 element retrotransposition. Proc Natl Acad Sci USA 88:936-940 (1991).
9. Curcio MJ, Garfinkel DJ: New lines of host defense: inhibition of Ty1 retrotransposition by Fus3p and NER/TFIIH. Trends Genet 15:43-45 (1999).
10. Delneri D, Colson I, Grammenoudi S, Roberts IN, Louis EJ, Oliver SG: Engineering evolution to study speciation in yeasts. Nature 422:68-72 (2003).
11. Derr LK: The involvement of cellular recombination and repair genes in RNA-mediated recombination in Saccharomyces cerevisiae. Genetics 148:937-945 (1998).
12. Derr LK, Strathern JN: A role for reverse transcripts in gene conversion. Nature 361:170-173 (1993).
13. Derr LK, Strathern JN, Garfinkel DJ: RNA-mediated recombination in S. cerevisiae. Cell 67:355-364 (1991).
14. Dombroski BA, Feng Q, Mathias SL, Sassaman DM, Scott AF, Kazazian HH, Jr, Boeke JD: An in vivo assay for the reverse transcriptase of human retrotransposon L1 in Saccharomyces cerevisiae. Mol Cell Biol 14:4485-4492 (1994).
15. Dunham MJ, Badrane H, Ferea T, Adams J, Brown PO, Rosenzweig F, Botstein D: Characteristic genome rearrangements in experimental evolution of Saccharomyces cerevisiae. Proc Natl Acad Sci USA 99:16144-16149 (2002).
16. Eichler EE, Sankoff D: Structural dynamics of eukaryotic chromosome evolution. Science 301:793-797 (2003).
17. Fink GR: Pseudogenes in yeast? Cell 49:5-6 (1987).
18. Fink G, Farabaugh P, Roeder G, Chaleff D: Transposable elements (Ty) in yeast. Cold Spring Harbor Symp Quant Biol 45:575-580 (1980).
19. Fischer G, James SA, Roberts IN, Oliver SG, Louis EJ: Chromosomal evolution in Saccharomyces. Nature 405:451-454 (2000).
20. Fischer G, Neuveglise C, Durrens P, Gaillardin C, Dujon B: Evolution of gene order in the genomes of two related yeast species. Genome Res 11:2009-2019 (2001).
21. Gaut BS, Le Thierry d'Ennequin M, Peek AS, Sawkins MC: Maize as a model for the evolution of plant nuclear genomes. Proc Natl Acad Sci USA 97:7008-7015 (2000).
22. Goffeau A, Barrell BG, Bussey H, Davis RW, Dujon B, Feldmann H, Galibert F, Hoheisel JD, Jacq C, Johnston M, Louis EJ, Mewes HW, Murakami Y, Philippsen P, Tettelin H, Oliver SG: Life with 6000 genes. Science 274:563-567 (1996).
23. Goodwin TJ, Poulter RT: Multiple LTR-retrotransposon families in the asexual yeast Candida albicans. Genome Res 10:174-191 (2000).
24. Hoppe GJ, Tanny JC, Rudner AD, Gerber SA, Danaie S, Gygi SP, Moazed D: Steps in assembly of silent chromatin in yeast: Sir3-independent binding of a Sir2/Sir4 complex to silencers and role for Sir2-dependent deacetylation. Mol Cell Biol 22:4167-4180 (2002).
25. Kalendar R, Tanskanen J, Immonen S, Nevo E, Schulman AH: Genome evolution of wild barley (Hordeum spontaneum) by BARE-1 retrotransposon dynamics in response to sharp microclimatic divergence. Proc Natl Acad Sci USA 97:6603-6607 (2000).
26. Kellis M, Patterson N, Endrizzi M, Birren B, Lander ES: Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423:241-254 (2003).
27. Kim JM, Vanguri S, Boeke JD, Gabriel A, Voytas DF: Transposable elements and genome organization: a comprehensive survey of retrotransposons revealed by the complete Saccharomyces cerevisiae genome sequence. Genome Res 8:464-478 (1998).
28. Kinsey JA: Transnuclear retrotransposition of the Tad element of Neurospora. Proc Natl Acad Sci USA 90:9384-9387 (1993).
29. Kinsey PT, Sandmeyer SB: Adjacent pol II and pol III promoters: transcription of the yeast retrotransposon Ty3 and a target tRNA gene. Nucleic Acids Res 19:1317-1324 (1991).
30. Knight SA, Labbe S, Kwon LF, Kosman DJ, Thiele DJ: A widespread transposable element masks expression of a yeast copper transport gene. Genes Dev 10:1917-1929 (1996).
31. Liebman SW, Singh A, Sherman F: A mutator affecting the region of the iso-1-cytochrome c gene in yeast. Genetics 92:783-802 (1979).
32. Liebman S, Shalit P, Picologlou S: Ty elements are involved in the formation of deletions in DEL1 strains of Saccharomyces cerevisiae. Cell 26:401-409 (1981).
33. Lynch M, Conery JS: The origins of genome complexity. Science 302:1401-1404 (2003).
34. Martin SL, Li J, Epperson LE, Lieberman B: Functional reverse transcriptases encoded by A-type mouse LINE-1: defining the minimal domain by deletion analysis. Gene 215:69-75 (1998).
35. Moffat AS: Transposons help sculpt a dynamic genome. Science 289:1455-1457 (2000).
36. Moore JK, Haber JE: Capture of retrotransposon DNA at the sites of chromosomal double-strand breaks. Nature 383:644-646 (1996).
37. Neuveglise C, Feldmann H, Bon E, Gaillardin C, Casaregola S: Genomic evolution of the long terminal repeat retrotransposons in hemiascomycetous yeasts. Genome Res 12:930-943 (2002).
38. Nissley DV, Garfinkel DJ, Strathem JN: HIV reverse transcription in yeast. Nature 380:30 (1996).
39. Paquin C, Adams J: Frequency of fixation of adaptive mutations is higher in evolving diploid than haploid yeast populations. Nature 302:495-500 (1983).
40. Paquin CE, Williamson VM: Temperature effects on the rate of Ty transposition. Science 226:53-55 (1984).
41. Paquin CE, Williamson VM: Ty insertions at two loci account for most of the spontaneous antimycin A resistance mutations during growth at 15°C of Saccharomyces cerevisiae strains lacking ADH1. Mol Cell Biol 6:70-79 (1986).
42. Promislow DE, Jordan IK, McDonald JF: Genomic demography: a life-history analysis of transposable element evolution. Proc R Soc Lond B Biol Sci 266:1555-1560 (1999).
43. Qadri I, Siddiqui A: Expression of hepatitis B virus polymerase in Ty1-his3AI retroelement of Saccharomyces cerevisiae. J Biol Chem 274:31359-31365 (1999).
44. Querol A, Fernandez-Espinar MT, del Olmo M, Barrio E: Adaptive evolution of wine yeast. Int J Food Microbiol 86:3-10 (2003).
45. Rachidi N, Barre P, Blondin B: Multiple Ty-mediated chromosomal translocations lead to karyotype changes in a wine strain of Saccharomyces cerevisiae. Mol Gen Genet 261:841-850 (1999).
46. Rowley JD: The critical role of chromosome translocations in human leukemias. Annu Rev Genet 32:495-519 (1998).
47. Sandmeyer SB, Aye M, Menees T: Ty3, a position specific, gypsy-like element in Saccharomyces cerevisiae, in Craig NL, Craigie R, Gellert M, Lambowitz AM (eds): Mobile DNA II, pp 663-683 (ASM Press, Washington DC 2002).
48. SanMiguel P, Tikhonov A, Jin YK, Motchoulskaia N, Zakharov D, Melake-Berhan A, Springer PS, Edwards KJ, Lee M, Avramova Z, Bennetzen JL: Nested retrotransposons in the intergenic regions of the maize genome. Science 274:765-768 (1996).
49. SanMiguel P, Gaut BS, Tikhonov A, Nakajima Y, Bennetzen JL: The paleontology of intergene retrotransposons of maize. Nat Genet 20:43-45 (1998).
50. Smith V, Chou KN, Lashkari D, Botstein D, Brown PO: Functional analysis of the genes of yeast chromosome V by genetic footprinting. Science 274:2069-2074 (1996).
51. Teng SC, Kim B, Gabriel A: Retrotransposon reverse-transcriptase-mediated repair of chromosomal breaks. Nature 383:641-644 (1996).
52. Voytas DF: Retroelements in genome organization. Science 274:737-738 (1996).
53. Voytas DF, Boeke JD: Ty1 and Ty5 of Saccharomyces cerevisiae, in Craig NL, Craigie R, Gellert M, Lambowitz AM (eds): Mobile DNA II, pp 631-662 (ASM Press, Washington DC 2002).
54. Weinstock KG, Mastrangelo MF, Burkett TJ, Garfinkel DJ, Strathern JN: Multimeric arrays of the yeast retrotransposon Ty. Mol Cell Biol 10:2882-2892 (1990).
55. Wilke CM, Adams J: Fitness effects of Ty transposition in Saccharomyces cerevisiae. Genetics 131:31-42 (1992).
56. Wilke CM, Maimer E, Adams J: The population biology and evolutionary significance of Ty elements in Saccharomyces cerevisiae. Genetica 86:155-173 (1992).
57. Williamson VM, Paquin CE: Homology of Saccharomyces cerevisiae ADH4 to an iron-activated alcohol dehydrogenase from Zymomonas mobilis. Mol Gen Genet 209:374-381 (1987).
58. Winston F, Chaleff DT, Valent B, Fink GR: Mutations affecting Ty-mediated expression of the HIS4 gene of Saccharomyces cerevisiae. Genetics 107:179-197 (1984).
59. Wolfe KH, Shields DC: Molecular evidence for an ancient duplication of the entire yeast genome. Nature 387:708-713 (1997).
60. Wong S, Butler G, Wolfe KH: Gene order evolution and paleopolyploidy in hemiascomycete yeasts. Proc Natl Acad Sci USA 99:9272-9277 (2002).
61. Yu X, Gabriel A: Patching broken chromosomes with extranuclear cellular DNA. Mol Cell 4:873-881 (1999).
62. Zou S, Wright DA, Voytas DF: The Saccharomyces Ty5 retrotransposon family is associated with origins of DNA replication at the telomeres and the silent mating locus HMR. Proc Natl Acad Sci USA 92:920-924 (1995).