Retrotransposon overdose and genome integrity

Proceedings of the National Academy of Sciences of the United States of America

Volumn 106, Issue 33, 2009, Pages 13927-13932

  Scheifele, Lisa Z ^a,b   Cost, Gregory J ^a,c   Zupancic, Margaret L ^a   Caputo, Emerita M ^a   Boeke, Jef D ^a  

^a JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b LOYOLA UNIVERSITY MARYLAND   (United States)

^c SANGAMO BIOSCIENCES INC   (United States)

Author keywords

Chromosome rearrangement; Genome instability; Ty1 elements

Indexed keywords

ARTICLE; CHROMOSOME ABERRATION; DNA DAMAGE; DNA REPLICATION; FUNGAL GENE; FUNGAL GENOME; FUNGUS GROWTH; GENE IDENTIFICATION; GENOMIC INSTABILITY; NONHUMAN; PRIORITY JOURNAL; RETROPOSON; SACCHAROMYCES CEREVISIAE;

CHROMOSOMES, FUNGAL; DNA DAMAGE; DNA REPAIR; DNA REPLICATION; DNA, FUNGAL; FUNGAL PROTEINS; GENE REARRANGEMENT; GENOME; GENOME, FUNGAL; MODELS, GENETIC; PLASMIDS; RECOMBINATION, GENETIC; RETROELEMENTS; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS;

MAMMALIA; SACCHAROMYCES CEREVISIAE;

EID: 69549090360     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0906552106     Document Type: Article

References (40)

1. Pan X, et al. (2006) A DNA integrity network in the yeast Saccharomyces cerevisiae. Cell 124:1069-1081. (Pubitemid 43344244)
2. Collins SR, et al. (2007) Functional dissection of protein complexes involved in yeast chromosome biology using a genetic interaction map. Nature 446:806-810.
3. Tong AH, et al. (2004) Global mapping of the yeast genetic interaction network. Science 303:808-813. (Pubitemid 38174652)
4. Kobayashi T (2006) Strategies to maintain the stability of the ribosomal RNA gene repeats-collaboration of recombination, cohesion and condensation. Genes Genet Syst 81:155-161.
5. Lenzmeier BA, Freundereich CH (2003) Trinucleotide repeat instability: a hairpin curve at the crossroads of replication, recombination, and repair. Cytogenet Genome Res 100:7-24.
6. Kim JM, Vanguri S, Boeke JD, Gabriel A, Voytas DF (1998) Transposable elements and genome organization: a comprehensive survey of retrotransposons revealed by the complete Saccharomyces cerevisiae genome sequence. Genome Res 8:464-478. (Pubitemid 28256796)
7. Boeke JD, Sandmeyer SB (1991) Yeast transposable elements. The Molecular and Cellular Biology of the Yeast Saccharomyces, ed Broach J, Jones E, Pringle J (Cold Spring Harbor Lab Press, Cold Spring Harbor, NY), pp 193-261.
8. Lesage P, Todeschini AL (2005) Happy together: the life and times of Ty retrotransposons and their hosts. Cytogenet Genome Res 110:70-90. (Pubitemid 41159885)
9. Lemoine FJ, Degtyareva NP, Lobachev K, Petes TD (2005) Chromosomal translocations in yeast induced by low levels of DNA polymerase amodel for chromosome fragile sites. Cell 120:587-598. (Pubitemid 40343072)
10. Admire A, et al. (2006) Cycles of chromosome instability are associated with a fragile site and are increased by defects in DNA replication and checkpoint controls in yeast. Genes Dev 20:159-173. (Pubitemid 43112935)
11. Lambert S, Watson A, Sheedy DM, Martin B, Carr AM (2005) Gross chromosomal rearrangements and elevated recombination at an inducible site-specific replication fork barrier. Cell 121:689-702. (Pubitemid 40797592)
12. Rachidi N, Barre P, Blondin B (1999) Multiple Ty-mediated chromosomal translocations lead to karyotype changes in a wine strain of Saccharomyces cerevisiae. Mol Gen Genet 261:841-850. (Pubitemid 29286764)
13. Fischer G, James SA, Roberts IN, Oliver SG, Louis EJ (2000) Chromosomal evolution in Saccharomyces. Nature 405:451-454.
14. Umezu K, Hiraoka M, Mori M, Maki H (2002) Structural analysis of aberrant chromosomes that occur spontaneously in diploid Saccharomyces cerevisiae: retrotransposon Ty1 plays a crucial role in chromosomal rearrangements. Genetics 160:97-110. (Pubitemid 34118274)
15. Koszul R, Caburet S, Dujon B, Fischer G (2004) Eucaryotic genome evolution through the spontaneous duplication of large chromosomal segments. EMBO J 23:234-243. (Pubitemid 38165763)
16. Adams J, Oeller PW (1986) Structure of evolving populations of Saccharomyces cerevisiae: adaptive changes are frequently associated with sequence alterations involving mobile elements belonging to the Ty family. Proc Natl Acad Sci USA 83:7124-7127. (Pubitemid 16002381)
17. Dunham MJ, et al. (2002) Characteristic genome rearrangements in experimental evolution of Saccharomyces cerevisiae. Proc Natl Acad Sci USA 99:16144-16149.
18. Kupiec M, Petes TD (1988) Allelic and ectopic recombination between Ty elements in yeast. Genetics 119:549-559.
19. Garfinkel DJ, Nyswaner KM, Stefanisko KM, Chang C, Moore SP (2005) Ty1 copy number dynamics in Saccharomyces. Genetics 169:1845-1857. (Pubitemid 40695602)
20. Boeke JD, Eichinger DJ, Natsoulis G (1991b) Doubling Ty1 element copy number in Saccharomyces cerevisiae: host genome stability and phenotypic effects. Genetics 129:1043-1052.
21. Wilke CM, Adams J (1992) Fitness effects of Ty transposition in Saccharomyces cerevisiae. Genetics 131:31-42.
22. Ji H, et al. (1993) Hotspots for unselected Ty1 transposition events on yeast chromosome III are near tRNA genes and LTR sequences. Cell 73:1007-1018. (Pubitemid 23165615)
23. Cost GJ, Boeke JD (1996) A useful colony colour phenotype associated with the yeast selectable/counter-selectable marker MET15. Yeast 12:939-941.
24. Hicks J, Strathern J, Klar A, Ismail S, Broach J (1984) Structure of the SAD mutation and the location of control sites at silent mating type genes in Saccharomyces cerevisiae. Mol Cell Biol 4:1278-1285. (Pubitemid 16242524)
25. Scholes DT, Banerjee M, Bowen B, Curcio MJ (2001) Multiple regulators of Ty1 transposition in Saccharomyces cerevisiae have conserved roles in genome maintenance. Genetics 159:1449-1465. (Pubitemid 34087588)
26. Holmes AM, Haber JE (1999) Double-strand break repair in yeast requires both leading and lagging strand DNA polymerases. Cell 96:415-424.
27. Gutierrez PJ, Wang TS (2003) Genomic instability induced by mutations in Saccharomyces cerevisiae POL1. Genetics 165:65-81.
28. Wicksteed BL, et al. (1994) A physical comparison of chromosome III in six strains of Saccharomyces cerevisiae. Yeast 10:39-57. (Pubitemid 24052948)
29. Calzada A, Hodgson B, Kanemaki M, Bueno A, Labib K (2005) Molecular anatomy and regulation of a stable replisome at a paused eukaryotic DNA replication fork. Genes Dev 19:1905-1919. (Pubitemid 41186991)
30. Bermudez VP, et al. (2003) The alternative Ctf18-Dcc1-Ctf8-replication factor C complex required for sister chromatid cohesion loads proliferating cell nuclear antigen onto DNA. Proc Natl Acad Sci USA 100:10237-10242.
31. Tercero JA, Diffley JF (2001) Regulation of DNA replication fork progression through damaged DNA by the Mec1/Rad53 checkpoint. Nature 412:553-557.
32. Cha RS, Kleckner N (2002) ATR homolog Mec1 promotes fork progression, thus averting breaks in replication slow zones. Science 297:602-606.
33. Cobb JA, et al. (2005) Replisome instability, fork collapse, and gross chromosomal rearrangements arise synergistically from Mec1 kinase and RecQ helicase mutations. Genes Dev 19:3055-3069.
34. Brewer BJ, Fangman WL (1988) A replication fork barrier at the 3′ end of yeast ribosomal RNA genes. Cell 55:637-643.
35. McMurray MA, Gottschling DE (2003) An age-induced switch to a hyper-recombinational state. Science 301:1908-1911.
36. Kobayashi T, Heck DJ, Nomura M, Horiuchi T (1998) Expansion and contraction of ribosomal DNA repeats in Saccharomyces cerevisiae: requirement of replication fork blocking (Fob1) protein and the role of RNA polymerase I. Genes Dev 12:3821-3830. (Pubitemid 29024845)
37. Wheelan SJ, Scheifele LZ, Martinez-Murillo F, Irizarry RA, Boeke JD (2006) Transposon insertion site profiling chip (TIP-chip). Proc Natl Acad Sci USA 103:17632-17637. (Pubitemid 44852212)
38. Deshpande AM, Newlon CS (1996) DNA replication fork pause sites dependent on transcription. Science 272:1030-1033.
39. Sherman F, Fink GR, Hicks JB (1986) Methods in Yeast Genetics (Cold Spring Harbor Lab Press, Cold Spring Harbor, NY).
40. Ludwig DL, Bruschi CV (1991) The 2-micron plasmid as a nonselectable, stable, high copy number yeast vector. Plasmid 25:81-95.