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. 1995 May;140(1):67–77. doi: 10.1093/genetics/140.1.67

Recombination of Ty Elements in Yeast Can Be Induced by a Double-Strand Break

A Parket 1, O Inbar 1, M Kupiec 1
PMCID: PMC1206572  PMID: 7635309

Abstract

The Ty retrotransposons are the main family of dispersed repeated sequences in the yeast Saccharomyces cerevisiae. These elements are flanked by a pair of long terminal direct repeats (LTRs). Previous experiments have shown that Ty elements recombine at low frequencies, despite the fact that they are present in 30 copies per genome. This frequency is not highly increased by treatments that cause DNA damage, such as UV irradiation. In this study, we show that it is possible to increase the recombination level of a genetically marked Ty by creating a double-strand break in it. This break is repaired by two competing mechanisms: one of them leaves a single LTR in place of the Ty, and the other is a gene conversion event in which the marked Ty is replaced by an ectopically located one. In a strain in which the marked Ty has only one LTR, the double-strand break is repaired by conversion. We have also measured the efficiency of repair and monitored the progression of the cells through the cell-cycle. We found that in the presence of a double-strand break in the marked Ty, a proportion of the cells is unable to resume growth.

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Selected References

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  1. Bennett C. B., Lewis A. L., Baldwin K. K., Resnick M. A. Lethality induced by a single site-specific double-strand break in a dispensable yeast plasmid. Proc Natl Acad Sci U S A. 1993 Jun 15;90(12):5613–5617. doi: 10.1073/pnas.90.12.5613. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Boeke J. D., Eichinger D., Castrillon D., Fink G. R. The Saccharomyces cerevisiae genome contains functional and nonfunctional copies of transposon Ty1. Mol Cell Biol. 1988 Apr;8(4):1432–1442. doi: 10.1128/mcb.8.4.1432. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Fairhead C., Dujon B. Consequences of unique double-stranded breaks in yeast chromosomes: death or homozygosis. Mol Gen Genet. 1993 Aug;240(2):170–178. doi: 10.1007/BF00277054. [DOI] [PubMed] [Google Scholar]
  4. Fishman-Lobell J., Haber J. E. Removal of nonhomologous DNA ends in double-strand break recombination: the role of the yeast ultraviolet repair gene RAD1. Science. 1992 Oct 16;258(5081):480–484. doi: 10.1126/science.1411547. [DOI] [PubMed] [Google Scholar]
  5. Fishman-Lobell J., Rudin N., Haber J. E. Two alternative pathways of double-strand break repair that are kinetically separable and independently modulated. Mol Cell Biol. 1992 Mar;12(3):1292–1303. doi: 10.1128/mcb.12.3.1292. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Haber J. E. Mating-type gene switching in Saccharomyces cerevisiae. Trends Genet. 1992 Dec;8(12):446–452. doi: 10.1016/0168-9525(92)90329-3. [DOI] [PubMed] [Google Scholar]
  7. Jinks-Robertson S., Petes T. D. Chromosomal translocations generated by high-frequency meiotic recombination between repeated yeast genes. Genetics. 1986 Nov;114(3):731–752. doi: 10.1093/genetics/114.3.731. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Klar A. J., Strathern J. N., Broach J. R., Hicks J. B. Regulation of transcription in expressed and unexpressed mating type cassettes of yeast. Nature. 1981 Jan 22;289(5795):239–244. doi: 10.1038/289239a0. [DOI] [PubMed] [Google Scholar]
  9. Kostriken R., Heffron F. The product of the HO gene is a nuclease: purification and characterization of the enzyme. Cold Spring Harb Symp Quant Biol. 1984;49:89–96. doi: 10.1101/sqb.1984.049.01.012. [DOI] [PubMed] [Google Scholar]
  10. Kostriken R., Strathern J. N., Klar A. J., Hicks J. B., Heffron F. A site-specific endonuclease essential for mating-type switching in Saccharomyces cerevisiae. Cell. 1983 Nov;35(1):167–174. doi: 10.1016/0092-8674(83)90219-2. [DOI] [PubMed] [Google Scholar]
  11. Kupiec M., Petes T. D. Allelic and ectopic recombination between Ty elements in yeast. Genetics. 1988 Jul;119(3):549–559. doi: 10.1093/genetics/119.3.549. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Kupiec M., Petes T. D. Meiotic recombination between repeated transposable elements in Saccharomyces cerevisiae. Mol Cell Biol. 1988 Jul;8(7):2942–2954. doi: 10.1128/mcb.8.7.2942. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Lin F. L., Sperle K., Sternberg N. Intermolecular recombination between DNAs introduced into mouse L cells is mediated by a nonconservative pathway that leads to crossover products. Mol Cell Biol. 1990 Jan;10(1):103–112. doi: 10.1128/mcb.10.1.103. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Malone R. E., Esposito R. E. The RAD52 gene is required for homothallic interconversion of mating types and spontaneous mitotic recombination in yeast. Proc Natl Acad Sci U S A. 1980 Jan;77(1):503–507. doi: 10.1073/pnas.77.1.503. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Maryon E., Carroll D. Characterization of recombination intermediates from DNA injected into Xenopus laevis oocytes: evidence for a nonconservative mechanism of homologous recombination. Mol Cell Biol. 1991 Jun;11(6):3278–3287. doi: 10.1128/mcb.11.6.3278. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. McGill C. B., Shafer B. K., Derr L. K., Strathern J. N. Recombination initiated by double-strand breaks. Curr Genet. 1993;23(4):305–314. doi: 10.1007/BF00310891. [DOI] [PubMed] [Google Scholar]
  17. Melamed C., Kupiec M. Effect of donor copy number on the rate of gene conversion in the yeast Saccharomyces cerevisiae. Mol Gen Genet. 1992 Oct;235(1):97–103. doi: 10.1007/BF00286186. [DOI] [PubMed] [Google Scholar]
  18. Melamed C., Nevo Y., Kupiec M. Involvement of cDNA in homologous recombination between Ty elements in Saccharomyces cerevisiae. Mol Cell Biol. 1992 Apr;12(4):1613–1620. doi: 10.1128/mcb.12.4.1613. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Nasmyth K. A. The regulation of yeast mating-type chromatin structure by SIR: an action at a distance affecting both transcription and transposition. Cell. 1982 Sep;30(2):567–578. doi: 10.1016/0092-8674(82)90253-7. [DOI] [PubMed] [Google Scholar]
  20. Nevo-Caspi Y., Kupiec M. Transcriptional induction of Ty recombination in yeast. Proc Natl Acad Sci U S A. 1994 Dec 20;91(26):12711–12715. doi: 10.1073/pnas.91.26.12711. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Nickoloff J. A., Chen E. Y., Heffron F. A 24-base-pair DNA sequence from the MAT locus stimulates intergenic recombination in yeast. Proc Natl Acad Sci U S A. 1986 Oct;83(20):7831–7835. doi: 10.1073/pnas.83.20.7831. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Nickoloff J. A., Singer J. D., Hoekstra M. F., Heffron F. Double-strand breaks stimulate alternative mechanisms of recombination repair. J Mol Biol. 1989 Jun 5;207(3):527–541. doi: 10.1016/0022-2836(89)90462-2. [DOI] [PubMed] [Google Scholar]
  23. Ozenberger B. A., Roeder G. S. A unique pathway of double-strand break repair operates in tandemly repeated genes. Mol Cell Biol. 1991 Mar;11(3):1222–1231. doi: 10.1128/mcb.11.3.1222. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Parket A., Kupiec M. Ectopic recombination between Ty elements in Saccharomyces cerevisiae is not induced by DNA damage. Mol Cell Biol. 1992 Oct;12(10):4441–4448. doi: 10.1128/mcb.12.10.4441. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Plessis A., Perrin A., Haber J. E., Dujon B. Site-specific recombination determined by I-SceI, a mitochondrial group I intron-encoded endonuclease expressed in the yeast nucleus. Genetics. 1992 Mar;130(3):451–460. doi: 10.1093/genetics/130.3.451. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Raveh D., Hughes S. H., Shafer B. K., Strathern J. N. Analysis of the HO-cleaved MAT DNA intermediate generated during the mating type switch in the yeast Saccharomyces cerevisiae. Mol Gen Genet. 1989 Dec;220(1):33–42. [PubMed] [Google Scholar]
  27. Ray A., Machin N., Stahl F. W. A DNA double chain break stimulates triparental recombination in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A. 1989 Aug;86(16):6225–6229. doi: 10.1073/pnas.86.16.6225. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Ray A., Siddiqi I., Kolodkin A. L., Stahl F. W. Intra-chromosomal gene conversion induced by a DNA double-strand break in Saccharomyces cerevisiae. J Mol Biol. 1988 May 20;201(2):247–260. doi: 10.1016/0022-2836(88)90136-2. [DOI] [PubMed] [Google Scholar]
  29. Rothstein R., Helms C., Rosenberg N. Concerted deletions and inversions are caused by mitotic recombination between delta sequences in Saccharomyces cerevisiae. Mol Cell Biol. 1987 Mar;7(3):1198–1207. doi: 10.1128/mcb.7.3.1198. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Rudin N., Sugarman E., Haber J. E. Genetic and physical analysis of double-strand break repair and recombination in Saccharomyces cerevisiae. Genetics. 1989 Jul;122(3):519–534. doi: 10.1093/genetics/122.3.519. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Silberman R., Kupiec M. Plasmid-mediated induction of recombination in yeast. Genetics. 1994 May;137(1):41–48. doi: 10.1093/genetics/137.1.41. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Sugawara N., Haber J. E. Characterization of double-strand break-induced recombination: homology requirements and single-stranded DNA formation. Mol Cell Biol. 1992 Feb;12(2):563–575. doi: 10.1128/mcb.12.2.563. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Waldman A. S. The search for homology does not limit the rate of extrachromosomal homologous recombination in mammalian cells. Genetics. 1994 Feb;136(2):597–605. doi: 10.1093/genetics/136.2.597. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Weiffenbach B., Haber J. E. Homothallic switching of Saccharomyces cerevisiae mating type genes by using a donor containing a large internal deletion. Mol Cell Biol. 1985 Aug;5(8):2154–2158. doi: 10.1128/mcb.5.8.2154. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Weinert T. A., Hartwell L. H. The RAD9 gene controls the cell cycle response to DNA damage in Saccharomyces cerevisiae. Science. 1988 Jul 15;241(4863):317–322. doi: 10.1126/science.3291120. [DOI] [PubMed] [Google Scholar]
  36. Weinert T. A., Kiser G. L., Hartwell L. H. Mitotic checkpoint genes in budding yeast and the dependence of mitosis on DNA replication and repair. Genes Dev. 1994 Mar 15;8(6):652–665. doi: 10.1101/gad.8.6.652. [DOI] [PubMed] [Google Scholar]
  37. White C. I., Haber J. E. Intermediates of recombination during mating type switching in Saccharomyces cerevisiae. EMBO J. 1990 Mar;9(3):663–673. doi: 10.1002/j.1460-2075.1990.tb08158.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Wilson J. H., Leung W. Y., Bosco G., Dieu D., Haber J. E. The frequency of gene targeting in yeast depends on the number of target copies. Proc Natl Acad Sci U S A. 1994 Jan 4;91(1):177–181. doi: 10.1073/pnas.91.1.177. [DOI] [PMC free article] [PubMed] [Google Scholar]

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