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. 2001 May;158(1):155–166. doi: 10.1093/genetics/158.1.155

Expansions and contractions in 36-bp minisatellites by gene conversion in yeast.

F Pâques 1, G F Richard 1, J E Haber 1
PMCID: PMC1461658  PMID: 11333226

Abstract

The instability of simple tandem repeats, such as human minisatellite loci, has been suggested to arise by gene conversions. In Saccharomyces cerevisiae, a double-strand break (DSB) was created by the HO endonuclease so that DNA polymerases associated with gap repair must traverse an artificial minisatellite of perfect 36-bp repeats or a yeast Y' minisatellite containing diverged 36-bp repeats. Gene conversions are frequently accompanied by changes in repeat number when the template contains perfect repeats. When the ends of the DSB have nonhomologous tails of 47 and 70 nucleotides that must be removed before repair DNA synthesis can begin, 16% of gene conversions had rearrangements, most of which were contractions, almost always in the recipient locus. When efficient removal of nonhomologous tails was prevented in rad1 and msh2 strains, repair was reduced 10-fold, but among survivors there was a 10-fold reduction in contractions. Half the remaining events were expansions. A similar decrease in the contraction rate was observed when the template was modified so that DSB ends were homologous to the template; and here, too, half of the remaining rearrangements were expansions. In this case, efficient repair does not require RAD1 and MSH2, consistent with our previous observations. In addition, without nonhomologous DSB ends, msh2 and rad1 mutations did not affect the frequency or the distribution of rearrangements. We conclude that the presence of nonhomologous ends alters the mechanism of DSB repair, likely through early recruitment of repair proteins including Msh2p and Rad1p, resulting in more frequent contractions of repeated sequences.

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Selected References

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  1. Appelgren H., Cederberg H., Rannug U. Mutations at the human minisatellite MS32 integrated in yeast occur with high frequency in meiosis and involve complex recombination events. Mol Gen Genet. 1997 Sep;256(1):7–17. doi: 10.1007/s004380050540. [DOI] [PubMed] [Google Scholar]
  2. Armour J. A., Jeffreys A. J. Biology and applications of human minisatellite loci. Curr Opin Genet Dev. 1992 Dec;2(6):850–856. doi: 10.1016/s0959-437x(05)80106-6. [DOI] [PubMed] [Google Scholar]
  3. Balakumaran B. S., Freudenreich C. H., Zakian V. A. CGG/CCG repeats exhibit orientation-dependent instability and orientation-independent fragility in Saccharomyces cerevisiae. Hum Mol Genet. 2000 Jan 1;9(1):93–100. doi: 10.1093/hmg/9.1.93. [DOI] [PubMed] [Google Scholar]
  4. Baudat F., Manova K., Yuen J. P., Jasin M., Keeney S. Chromosome synapsis defects and sexually dimorphic meiotic progression in mice lacking Spo11. Mol Cell. 2000 Nov;6(5):989–998. doi: 10.1016/s1097-2765(00)00098-8. [DOI] [PubMed] [Google Scholar]
  5. Bergerat A., de Massy B., Gadelle D., Varoutas P. C., Nicolas A., Forterre P. An atypical topoisomerase II from Archaea with implications for meiotic recombination. Nature. 1997 Mar 27;386(6623):414–417. doi: 10.1038/386414a0. [DOI] [PubMed] [Google Scholar]
  6. Bishop A. J., Louis E. J., Borts R. H. Minisatellite variants generated in yeast meiosis involve DNA removal during gene conversion. Genetics. 2000 Sep;156(1):7–20. doi: 10.1093/genetics/156.1.7. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Borts R. H., Leung W. Y., Kramer W., Kramer B., Williamson M., Fogel S., Haber J. E. Mismatch repair-induced meiotic recombination requires the pms1 gene product. Genetics. 1990 Mar;124(3):573–584. doi: 10.1093/genetics/124.3.573. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Buard J., Bourdet A., Yardley J., Dubrova Y., Jeffreys A. J. Influences of array size and homogeneity on minisatellite mutation. EMBO J. 1998 Jun 15;17(12):3495–3502. doi: 10.1093/emboj/17.12.3495. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Buard J., Jeffreys A. J. Big, bad minisatellites. Nat Genet. 1997 Apr;15(4):327–328. doi: 10.1038/ng0497-327. [DOI] [PubMed] [Google Scholar]
  10. Buard J., Vergnaud G. Complex recombination events at the hypermutable minisatellite CEB1 (D2S90). EMBO J. 1994 Jul 1;13(13):3203–3210. doi: 10.1002/j.1460-2075.1994.tb06619.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Chen D. C., Yang B. C., Kuo T. T. One-step transformation of yeast in stationary phase. Curr Genet. 1992 Jan;21(1):83–84. doi: 10.1007/BF00318659. [DOI] [PubMed] [Google Scholar]
  12. Clikeman J. A., Wheeler S. L., Nickoloff J. A. Efficient incorporation of large (>2 kb) heterologies into heteroduplex DNA: Pms1/Msh2-dependent and -independent large loop mismatch repair in Saccharomyces cerevisiae. Genetics. 2001 Apr;157(4):1481–1491. doi: 10.1093/genetics/157.4.1481. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Colaiácovo M. P., Pâques F., Haber J. E. Removal of one nonhomologous DNA end during gene conversion by a RAD1- and MSH2-independent pathway. Genetics. 1999 Apr;151(4):1409–1423. doi: 10.1093/genetics/151.4.1409. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Correll C. C., Freeborn B., Moore P. B., Steitz T. A. Metals, motifs, and recognition in the crystal structure of a 5S rRNA domain. Cell. 1997 Nov 28;91(5):705–712. doi: 10.1016/s0092-8674(00)80457-2. [DOI] [PubMed] [Google Scholar]
  15. Datta A., Adjiri A., New L., Crouse G. F., Jinks Robertson S. Mitotic crossovers between diverged sequences are regulated by mismatch repair proteins in Saccaromyces cerevisiae. Mol Cell Biol. 1996 Mar;16(3):1085–1093. doi: 10.1128/mcb.16.3.1085. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Datta A., Hendrix M., Lipsitch M., Jinks-Robertson S. Dual roles for DNA sequence identity and the mismatch repair system in the regulation of mitotic crossing-over in yeast. Proc Natl Acad Sci U S A. 1997 Sep 2;94(18):9757–9762. doi: 10.1073/pnas.94.18.9757. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Debrauwère H., Buard J., Tessier J., Aubert D., Vergnaud G., Nicolas A. Meiotic instability of human minisatellite CEB1 in yeast requires DNA double-strand breaks. Nat Genet. 1999 Nov;23(3):367–371. doi: 10.1038/15557. [DOI] [PubMed] [Google Scholar]
  18. Evans E., Sugawara N., Haber J. E., Alani E. The Saccharomyces cerevisiae Msh2 mismatch repair protein localizes to recombination intermediates in vivo. Mol Cell. 2000 May;5(5):789–799. doi: 10.1016/s1097-2765(00)80319-6. [DOI] [PubMed] [Google Scholar]
  19. Ferguson D. O., Holloman W. K. Recombinational repair of gaps in DNA is asymmetric in Ustilago maydis and can be explained by a migrating D-loop model. Proc Natl Acad Sci U S A. 1996 May 28;93(11):5419–5424. doi: 10.1073/pnas.93.11.5419. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. 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]
  21. Freudenreich C. H., Stavenhagen J. B., Zakian V. A. Stability of a CTG/CAG trinucleotide repeat in yeast is dependent on its orientation in the genome. Mol Cell Biol. 1997 Apr;17(4):2090–2098. doi: 10.1128/mcb.17.4.2090. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Fu Y. H., Kuhl D. P., Pizzuti A., Pieretti M., Sutcliffe J. S., Richards S., Verkerk A. J., Holden J. J., Fenwick R. G., Jr, Warren S. T. Variation of the CGG repeat at the fragile X site results in genetic instability: resolution of the Sherman paradox. Cell. 1991 Dec 20;67(6):1047–1058. doi: 10.1016/0092-8674(91)90283-5. [DOI] [PubMed] [Google Scholar]
  23. Gacy A. M., Goellner G., Juranić N., Macura S., McMurray C. T. Trinucleotide repeats that expand in human disease form hairpin structures in vitro. Cell. 1995 May 19;81(4):533–540. doi: 10.1016/0092-8674(95)90074-8. [DOI] [PubMed] [Google Scholar]
  24. Hewett D. R., Handt O., Hobson L., Mangelsdorf M., Eyre H. J., Baker E., Sutherland G. R., Schuffenhauer S., Mao J. I., Richards R. I. FRA10B structure reveals common elements in repeat expansion and chromosomal fragile site genesis. Mol Cell. 1998 May;1(6):773–781. doi: 10.1016/s1097-2765(00)80077-5. [DOI] [PubMed] [Google Scholar]
  25. Holmes A. M., Haber J. E. Double-strand break repair in yeast requires both leading and lagging strand DNA polymerases. Cell. 1999 Feb 5;96(3):415–424. doi: 10.1016/s0092-8674(00)80554-1. [DOI] [PubMed] [Google Scholar]
  26. Horowitz H., Haber J. E. Subtelomeric regions of yeast chromosomes contain a 36 base-pair tandemly repeated sequence. Nucleic Acids Res. 1984 Sep 25;12(18):7105–7121. doi: 10.1093/nar/12.18.7105. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Ireland M. J., Reinke S. S., Livingston D. M. The impact of lagging strand replication mutations on the stability of CAG repeat tracts in yeast. Genetics. 2000 Aug;155(4):1657–1665. doi: 10.1093/genetics/155.4.1657. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Ivanov E. L., Haber J. E. RAD1 and RAD10, but not other excision repair genes, are required for double-strand break-induced recombination in Saccharomyces cerevisiae. Mol Cell Biol. 1995 Apr;15(4):2245–2251. doi: 10.1128/mcb.15.4.2245. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Jeffreys A. J., Tamaki K., MacLeod A., Monckton D. G., Neil D. L., Armour J. A. Complex gene conversion events in germline mutation at human minisatellites. Nat Genet. 1994 Feb;6(2):136–145. doi: 10.1038/ng0294-136. [DOI] [PubMed] [Google Scholar]
  30. Keeney S., Giroux C. N., Kleckner N. Meiosis-specific DNA double-strand breaks are catalyzed by Spo11, a member of a widely conserved protein family. Cell. 1997 Feb 7;88(3):375–384. doi: 10.1016/s0092-8674(00)81876-0. [DOI] [PubMed] [Google Scholar]
  31. Kirkpatrick D. T., Petes T. D. Repair of DNA loops involves DNA-mismatch and nucleotide-excision repair proteins. Nature. 1997 Jun 26;387(6636):929–931. doi: 10.1038/43225. [DOI] [PubMed] [Google Scholar]
  32. Kolodner R. D., Marsischky G. T. Eukaryotic DNA mismatch repair. Curr Opin Genet Dev. 1999 Feb;9(1):89–96. doi: 10.1016/s0959-437x(99)80013-6. [DOI] [PubMed] [Google Scholar]
  33. Lalioti M. D., Scott H. S., Buresi C., Rossier C., Bottani A., Morris M. A., Malafosse A., Antonarakis S. E. Dodecamer repeat expansion in cystatin B gene in progressive myoclonus epilepsy. Nature. 1997 Apr 24;386(6627):847–851. doi: 10.1038/386847a0. [DOI] [PubMed] [Google Scholar]
  34. Malter H. E., Iber J. C., Willemsen R., de Graaff E., Tarleton J. C., Leisti J., Warren S. T., Oostra B. A. Characterization of the full fragile X syndrome mutation in fetal gametes. Nat Genet. 1997 Feb;15(2):165–169. doi: 10.1038/ng0297-165. [DOI] [PubMed] [Google Scholar]
  35. May C. A., Jeffreys A. J., Armour J. A. Mutation rate heterogeneity and the generation of allele diversity at the human minisatellite MS205 (D16S309). Hum Mol Genet. 1996 Nov;5(11):1823–1833. doi: 10.1093/hmg/5.11.1823. [DOI] [PubMed] [Google Scholar]
  36. McMurray C. T. DNA secondary structure: a common and causative factor for expansion in human disease. Proc Natl Acad Sci U S A. 1999 Mar 2;96(5):1823–1825. doi: 10.1073/pnas.96.5.1823. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Moore J. K., Haber J. E. Cell cycle and genetic requirements of two pathways of nonhomologous end-joining repair of double-strand breaks in Saccharomyces cerevisiae. Mol Cell Biol. 1996 May;16(5):2164–2173. doi: 10.1128/mcb.16.5.2164. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Pâques F., Haber J. E. Multiple pathways of recombination induced by double-strand breaks in Saccharomyces cerevisiae. Microbiol Mol Biol Rev. 1999 Jun;63(2):349–404. doi: 10.1128/mmbr.63.2.349-404.1999. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Pâques F., Haber J. E. Two pathways for removal of nonhomologous DNA ends during double-strand break repair in Saccharomyces cerevisiae. Mol Cell Biol. 1997 Nov;17(11):6765–6771. doi: 10.1128/mcb.17.11.6765. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Pâques F., Leung W. Y., Haber J. E. Expansions and contractions in a tandem repeat induced by double-strand break repair. Mol Cell Biol. 1998 Apr;18(4):2045–2054. doi: 10.1128/mcb.18.4.2045. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. Pâques F., Wegnez M. Deletions and amplifications of tandemly arranged ribosomal 5S genes internal to a P element occur at a high rate in a dysgenic context. Genetics. 1993 Oct;135(2):469–476. doi: 10.1093/genetics/135.2.469. [DOI] [PMC free article] [PubMed] [Google Scholar]
  42. Rayssiguier C., Thaler D. S., Radman M. The barrier to recombination between Escherichia coli and Salmonella typhimurium is disrupted in mismatch-repair mutants. Nature. 1989 Nov 23;342(6248):396–401. doi: 10.1038/342396a0. [DOI] [PubMed] [Google Scholar]
  43. Richard G. F., Dujon B., Haber J. E. Double-strand break repair can lead to high frequencies of deletions within short CAG/CTG trinucleotide repeats. Mol Gen Genet. 1999 Jun;261(4-5):871–882. doi: 10.1007/s004380050031. [DOI] [PubMed] [Google Scholar]
  44. Richard G. F., Pâques F. Mini- and microsatellite expansions: the recombination connection. EMBO Rep. 2000 Aug;1(2):122–126. doi: 10.1093/embo-reports/kvd031. [DOI] [PMC free article] [PubMed] [Google Scholar]
  45. Richards R. I., Sutherland G. R. Dynamic mutation: possible mechanisms and significance in human disease. Trends Biochem Sci. 1997 Nov;22(11):432–436. doi: 10.1016/s0968-0004(97)01108-0. [DOI] [PubMed] [Google Scholar]
  46. Robinett C. C., Straight A., Li G., Willhelm C., Sudlow G., Murray A., Belmont A. S. In vivo localization of DNA sequences and visualization of large-scale chromatin organization using lac operator/repressor recognition. J Cell Biol. 1996 Dec;135(6 Pt 2):1685–1700. doi: 10.1083/jcb.135.6.1685. [DOI] [PMC free article] [PubMed] [Google Scholar]
  47. Sandell L. L., Zakian V. A. Loss of a yeast telomere: arrest, recovery, and chromosome loss. Cell. 1993 Nov 19;75(4):729–739. doi: 10.1016/0092-8674(93)90493-a. [DOI] [PubMed] [Google Scholar]
  48. Selva E. M., New L., Crouse G. F., Lahue R. S. Mismatch correction acts as a barrier to homeologous recombination in Saccharomyces cerevisiae. Genetics. 1995 Mar;139(3):1175–1188. doi: 10.1093/genetics/139.3.1175. [DOI] [PMC free article] [PubMed] [Google Scholar]
  49. Sugawara N., Ira G., Haber J. E. DNA length dependence of the single-strand annealing pathway and the role of Saccharomyces cerevisiae RAD59 in double-strand break repair. Mol Cell Biol. 2000 Jul;20(14):5300–5309. doi: 10.1128/mcb.20.14.5300-5309.2000. [DOI] [PMC free article] [PubMed] [Google Scholar]
  50. Sugawara N., Pâques F., Colaiácovo M., Haber J. E. Role of Saccharomyces cerevisiae Msh2 and Msh3 repair proteins in double-strand break-induced recombination. Proc Natl Acad Sci U S A. 1997 Aug 19;94(17):9214–9219. doi: 10.1073/pnas.94.17.9214. [DOI] [PMC free article] [PubMed] [Google Scholar]
  51. Vergnaud G., Mariat D., Apiou F., Aurias A., Lathrop M., Lauthier V. The use of synthetic tandem repeats to isolate new VNTR loci: cloning of a human hypermutable sequence. Genomics. 1991 Sep;11(1):135–144. doi: 10.1016/0888-7543(91)90110-z. [DOI] [PubMed] [Google Scholar]
  52. Virtaneva K., D'Amato E., Miao J., Koskiniemi M., Norio R., Avanzini G., Franceschetti S., Michelucci R., Tassinari C. A., Omer S. Unstable minisatellite expansion causing recessively inherited myoclonus epilepsy, EPM1. Nat Genet. 1997 Apr;15(4):393–396. doi: 10.1038/ng0497-393. [DOI] [PubMed] [Google Scholar]
  53. Wach A., Brachat A., Pöhlmann R., Philippsen P. New heterologous modules for classical or PCR-based gene disruptions in Saccharomyces cerevisiae. Yeast. 1994 Dec;10(13):1793–1808. doi: 10.1002/yea.320101310. [DOI] [PubMed] [Google Scholar]
  54. Welch J. W., Maloney D. H., Fogel S. Gene conversions within the Cup1r region from heterologous crosses in Saccharomyces cerevisiae. Mol Gen Genet. 1991 Oct;229(2):261–266. doi: 10.1007/BF00272164. [DOI] [PubMed] [Google Scholar]
  55. Welch J. W., Maloney D. H., Fogel S. Unequal crossing-over and gene conversion at the amplified CUP1 locus of yeast. Mol Gen Genet. 1990 Jul;222(2-3):304–310. doi: 10.1007/BF00633833. [DOI] [PubMed] [Google Scholar]
  56. Yu A., Dill J., Mitas M. The purine-rich trinucleotide repeat sequences d(CAG)15 and d(GAC)15 form hairpins. Nucleic Acids Res. 1995 Oct 25;23(20):4055–4057. doi: 10.1093/nar/23.20.4055. [DOI] [PMC free article] [PubMed] [Google Scholar]
  57. Yu S., Mangelsdorf M., Hewett D., Hobson L., Baker E., Eyre H. J., Lapsys N., Le Paslier D., Doggett N. A., Sutherland G. R. Human chromosomal fragile site FRA16B is an amplified AT-rich minisatellite repeat. Cell. 1997 Feb 7;88(3):367–374. doi: 10.1016/s0092-8674(00)81875-9. [DOI] [PubMed] [Google Scholar]

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