[1] | Chen JM, Cooper DN, Ferec C, Kehrer-Sawatzki H, Patrinos GP (2010) Genomic rearrangements in inherited disease and cancer. Semin Cancer Biol 20: 222–233. doi: 10.1016/j.semcancer.2010.05.007
|
[2] | Agarwal S, Tafel AA, Kanaar R (2006) DNA double-strand break repair and chromosome translocations. DNA Repair (Amst) 5: 1075–1081. doi: 10.1016/j.dnarep.2006.05.029
|
[3] | Richardson C, Jasin M (2000) Frequent chromosomal translocations induced by DNA double-strand breaks. Nature 405: 697–700.
|
[4] | Khanna KK, Jackson SP (2001) DNA double-strand breaks: signaling, repair and the cancer connection. Nat Genet 27: 247–254.
|
[5] | Rothkamm K, Lobrich M (2002) Misrepair of radiation-induced DNA double-strand breaks and its relevance for tumorigenesis and cancer treatment (review). Int J Oncol 21: 433–440. doi: 10.3892/ijo.21.2.433
|
[6] | Bosco G, Haber JE (1998) Chromosome break-induced DNA replication leads to nonreciprocal translocations and telomere capture. Genetics 150: 1037–1047.
|
[7] | Kang LE, Symington LS (2000) Aberrant double-strand break repair in rad51 mutants of Saccharomyces cerevisiae. Mol Cell Biol 20: 9162–9172. doi: 10.1128/mcb.20.24.9162-9172.2000
|
[8] | Aguilera A (2001) Double-strand break repair: are Rad51/RecA–DNA joints barriers to DNA replication? Trends Genet 17: 318–321. doi: 10.1016/s0168-9525(01)02309-5
|
[9] | McEachern MJ, Haber JE (2006) Break-induced replication and recombinational telomere elongation in yeast. Annu Rev Biochem 75: 111–135. doi: 10.1146/annurev.biochem.74.082803.133234
|
[10] | Davis AP, Symington LS (2004) RAD51-dependent break-induced replication in yeast. Mol Cell Biol 24: 2344–2351. doi: 10.1128/mcb.24.6.2344-2351.2004
|
[11] | Malkova A, Naylor ML, Yamaguchi M, Ira G, Haber JE (2005) RAD51-dependent break-induced replication differs in kinetics and checkpoint responses from RAD51-mediated gene conversion. Mol Cell Biol 25: 933–944. doi: 10.1128/mcb.25.3.933-944.2005
|
[12] | Morrow DM, Connelly C, Hieter P (1997) “Break copy” duplication: a model for chromosome fragment formation in Saccharomyces cerevisiae. Genetics 147: 371–382.
|
[13] | Lydeard JR, Jain S, Yamaguchi M, Haber JE (2007) Break-induced replication and telomerase-independent telomere maintenance require Pol32. Nature 448: 820–823. doi: 10.1038/nature06047
|
[14] | Lydeard JR, Lipkin-Moore Z, Sheu YJ, Stillman B, Burgers PM, et al. (2010) Break-induced replication requires all essential DNA replication factors except those specific for pre-RC assembly. Genes Dev 24: 1133–1144. doi: 10.1101/gad.1922610
|
[15] | Hashimoto Y, Puddu F, Costanzo V (2012) RAD51- and MRE11-dependent reassembly of uncoupled CMG helicase complex at collapsed replication forks. Nat Struct Mol Biol 19: 17–24. doi: 10.1038/nsmb.2177
|
[16] | Smith CE, Llorente B, Symington LS (2007) Template switching during break-induced replication. Nature 447: 102–105. doi: 10.1038/nature05723
|
[17] | Lee JA, Carvalho CM, Lupski JR (2007) A DNA replication mechanism for generating nonrecurrent rearrangements associated with genomic disorders. Cell 131: 1235–1247. doi: 10.1016/j.cell.2007.11.037
|
[18] | Ruiz JF, Gomez-Gonzalez B, Aguilera A (2009) Chromosomal translocations caused by either Pol32-dependent or Pol32-independent triparental break-induced replication. Mol Cell Biol 29: 5441–5454. doi: 10.1128/mcb.00256-09
|
[19] | Schmidt KH, Viebranz E, Doerfler L, Lester C, Rubenstein A (2010) Formation of complex and unstable chromosomal translocations in yeast. PLoS ONE 5: e12007 doi:10.1371/journal.pone.0012007. doi: 10.1371/journal.pone.0012007
|
[20] | Liu P, Erez A, Nagamani SC, Dhar SU, Kolodziejska KE, et al. (2011) Chromosome catastrophes involve replication mechanisms generating complex genomic rearrangements. Cell 146: 889–903. doi: 10.1016/j.cell.2011.07.042
|
[21] | Zhang F, Khajavi M, Connolly AM, Towne CF, Batish SD, et al. (2009) The DNA replication FoSTeS/MMBIR mechanism can generate genomic, genic and exonic complex rearrangements in humans. Nat Genet 41: 849–853. doi: 10.1038/ng.399
|
[22] | Deem A, Barker K, Vanhulle K, Downing B, Vayl A, et al. (2008) Defective break-induced replication leads to half-crossovers in Saccharomyces cerevisiae. Genetics 179: 1845–1860. doi: 10.1534/genetics.108.087940
|
[23] | Smith CE, Lam AF, Symington LS (2009) Aberrant double-strand break repair resulting in half crossovers in mutants defective for Rad51 or the DNA polymerase delta complex. Mol Cell Biol 29: 1432–1441. doi: 10.1128/mcb.01469-08
|
[24] | Sabatier L, Ricoul M, Pottier G, Murnane JP (2005) The loss of a single telomere can result in instability of multiple chromosomes in a human tumor cell line. Mol Cancer Res 3: 139–150. doi: 10.1158/1541-7786.mcr-04-0194
|
[25] | Schwartz EK, Heyer WD (2011) Processing of joint molecule intermediates by structure-selective endonucleases during homologous recombination in eukaryotes. Chromosoma 120: 109–127. doi: 10.1007/s00412-010-0304-7
|
[26] | Ip SC, Rass U, Blanco MG, Flynn HR, Skehel JM, et al. (2008) Identification of Holliday junction resolvases from humans and yeast. Nature 456: 357–361. doi: 10.1038/nature07470
|
[27] | Matos J, Blanco MG, Maslen S, Skehel JM, West SC (2011) Regulatory Control of the Resolution of DNA Recombination Intermediates during Meiosis and Mitosis. Cell 147: 158–172. doi: 10.1016/j.cell.2011.08.032
|
[28] | Blanco MG, Matos J, Rass U, Ip SC, West SC (2010) Functional overlap between the structure-specific nucleases Yen1 and Mus81-Mms4 for DNA-damage repair in S. cerevisiae. DNA Repair (Amst) 9: 394–402. doi: 10.1016/j.dnarep.2009.12.017
|
[29] | Tay YD, Wu L (2010) Overlapping roles for Yen1 and Mus81 in cellular Holliday junction processing. J Biol Chem 285: 11427–11432. doi: 10.1074/jbc.m110.108399
|
[30] | Ho CK, Mazon G, Lam AF, Symington LS (2010) Mus81 and Yen1 promote reciprocal exchange during mitotic recombination to maintain genome integrity in budding yeast. Mol Cell 40: 988–1000. doi: 10.1016/j.molcel.2010.11.016
|
[31] | Agmon N, Yovel M, Harari Y, Liefshitz B, Kupiec M (2011) The role of Holliday junction resolvases in the repair of spontaneous and induced DNA damage. Nucleic Acids Res 39: 7009–7019. doi: 10.1093/nar/gkr277
|
[32] | Froget B, Blaisonneau J, Lambert S, Baldacci G (2008) Cleavage of stalled forks by fission yeast Mus81/Eme1 in absence of DNA replication checkpoint. Mol Biol Cell 19: 445–456. doi: 10.1091/mbc.e07-07-0728
|
[33] | Roseaulin L, Yamada Y, Tsutsui Y, Russell P, Iwasaki H, et al. (2008) Mus81 is essential for sister chromatid recombination at broken replication forks. Embo J 27: 1378–1387. doi: 10.1038/emboj.2008.65
|
[34] | Doe CL, Ahn JS, Dixon J, Whitby MC (2002) Mus81-Eme1 and Rqh1 involvement in processing stalled and collapsed replication forks. J Biol Chem 277: 32753–32759. doi: 10.1074/jbc.m202120200
|
[35] | Kaliraman V, Brill SJ (2002) Role of SGS1 and SLX4 in maintaining rDNA structure in Saccharomyces cerevisiae. Curr Genet 41: 389–400. doi: 10.1007/s00294-002-0319-6
|
[36] | Coulon S, Noguchi E, Noguchi C, Du LL, Nakamura TM, et al. (2006) Rad22Rad52-dependent repair of ribosomal DNA repeats cleaved by Slx1-Slx4 endonuclease. Mol Biol Cell 17: 2081–2090. doi: 10.1091/mbc.e05-11-1006
|
[37] | Coulon S, Gaillard PH, Chahwan C, McDonald WH, Yates JR 3rd, et al. (2004) Slx1-Slx4 are subunits of a structure-specific endonuclease that maintains ribosomal DNA in fission yeast. Mol Biol Cell 15: 71–80. doi: 10.1091/mbc.e03-08-0586
|
[38] | Zhang C, Roberts TM, Yang J, Desai R, Brown GW (2006) Suppression of genomic instability by SLX5 and SLX8 in Saccharomyces cerevisiae. DNA Repair (Amst) 5: 336–346. doi: 10.1016/j.dnarep.2005.10.010
|
[39] | Toh GW, Sugawara N, Dong J, Toth R, Lee SE, et al. (2010) Mec1/Tel1-dependent phosphorylation of Slx4 stimulates Rad1-Rad10-dependent cleavage of non-homologous DNA tails. DNA Repair (Amst) 9: 718–726. doi: 10.1016/j.dnarep.2010.02.013
|
[40] | Lyndaker AM, Goldfarb T, Alani E (2008) Mutants defective in Rad1-Rad10-Slx4 exhibit a unique pattern of viability during mating-type switching in Saccharomyces cerevisiae. Genetics 179: 1807–1821. doi: 10.1534/genetics.108.090654
|
[41] | Hwang JY, Smith S, Myung K (2005) The Rad1-Rad10 complex promotes the production of gross chromosomal rearrangements from spontaneous DNA damage in Saccharomyces cerevisiae. Genetics 169: 1927–1937. doi: 10.1534/genetics.104.039768
|
[42] | Pannunzio NR, Manthey GM, Bailis AM (2010) RAD59 and RAD1 cooperate in translocation formation by single-strand annealing in Saccharomyces cerevisiae. Curr Genet 56: 87–100. doi: 10.1007/s00294-009-0282-6
|
[43] | Haber JE (1998) Mating-type gene switching in Saccharomyces cerevisiae. Annu Rev Genet 32: 561–599. doi: 10.1146/annurev.genet.32.1.561
|
[44] | Lustig AJ (1998) Mechanisms of silencing in Saccharomyces cerevisiae. Curr Opin Genet Dev 8: 233–239. doi: 10.1016/s0959-437x(98)80146-9
|
[45] | Nickoloff JA, Singer JD, Heffron F (1990) In vivo analysis of the Saccharomyces cerevisiae HO nuclease recognition site by site-directed mutagenesis. Mol Cell Biol 10: 1174–1179.
|
[46] | Weiffenbach B, Rogers DT, Haber JE, Zoller M, Russell DW, et al. (1983) Deletions and single base pair changes in the yeast mating type locus that prevent homothallic mating type conversions. Proc Natl Acad Sci U S A 80: 3401–3405. doi: 10.1073/pnas.80.11.3401
|
[47] | Klar AJ, Strathern JN, Hicks JB, Prudente D (1983) Efficient production of a ring derivative of chromosome III by the mating-type switching mechanism in Saccharomyces cerevisiae. Mol Cell Biol 3: 803–810.
|
[48] | Strathern JN, Newlon CS, Herskowitz I, Hicks JB (1979) Isolation of a circular derivative of yeast chromosome III: implications for the mechanism of mating type interconversion. Cell 18: 309–319. doi: 10.1016/0092-8674(79)90050-3
|
[49] | Thrower DA, Bloom K (2001) Dicentric chromosome stretching during anaphase reveals roles of Sir2/Ku in chromatin compaction in budding yeast. Mol Biol Cell 12: 2800–2812. doi: 10.1091/mbc.12.9.2800
|
[50] | Flott S, Alabert C, Toh GW, Toth R, Sugawara N, et al. (2007) Phosphorylation of Slx4 by Mec1 and Tel1 regulates the single-strand annealing mode of DNA repair in budding yeast. Mol Cell Biol 27: 6433–6445. doi: 10.1128/mcb.00135-07
|
[51] | Flott S, Rouse J (2005) Slx4 becomes phosphorylated after DNA damage in a Mec1/Tel1-dependent manner and is required for repair of DNA alkylation damage. Biochem J 391: 325–333. doi: 10.1042/bj20050768
|
[52] | Fekairi S, Scaglione S, Chahwan C, Taylor ER, Tissier A, et al. (2009) Human SLX4 is a Holliday junction resolvase subunit that binds multiple DNA repair/recombination endonucleases. Cell 138: 78–89. doi: 10.1016/j.cell.2009.06.029
|
[53] | Gonzalez-Barrera S, Cortes-Ledesma F, Wellinger RE, Aguilera A (2003) Equal sister chromatid exchange is a major mechanism of double-strand break repair in yeast. Mol Cell 11: 1661–1671. doi: 10.1016/s1097-2765(03)00183-7
|
[54] | Kadyk LC, Hartwell LH (1992) Sister chromatids are preferred over homologs as substrates for recombinational repair in Saccharomyces cerevisiae. Genetics 132: 387–402.
|
[55] | Chabes A, Georgieva B, Domkin V, Zhao X, Rothstein R, et al. (2003) Survival of DNA damage in yeast directly depends on increased dNTP levels allowed by relaxed feedback inhibition of ribonucleotide reductase. Cell 112: 391–401. doi: 10.1016/s0092-8674(03)00075-8
|
[56] | Deem A, Keszthelyi A, Blackgrove T, Vayl A, Coffey B, et al. (2011) Break-induced replication is highly inaccurate. PLoS Biol 9: e1000594 doi:10.1371/journal.pbio.1000594. doi: 10.1371/journal.pbio.1000594
|
[57] | Hanada K, Budzowska M, Davies SL, van Drunen E, Onizawa H, et al. (2007) The structure-specific endonuclease Mus81 contributes to replication restart by generating double-strand DNA breaks. Nat Struct Mol Biol 14: 1096–1104. doi: 10.1038/nsmb1313
|
[58] | Zeng S, Xiang T, Pandita TK, Gonzalez-Suarez I, Gonzalo S, et al. (2009) Telomere recombination requires the MUS81 endonuclease. Nat Cell Biol 11: 616–623. doi: 10.1038/ncb1867
|
[59] | Ehmsen KT, Heyer WD (2008) Saccharomyces cerevisiae Mus81-Mms4 is a catalytic, DNA structure-selective endonuclease. Nucleic Acids Res 36: 2182–2195. doi: 10.1093/nar/gkm1152
|
[60] | Ehmsen KT, Heyer WD (2009) A junction branch point adjacent to a DNA backbone nick directs substrate cleavage by Saccharomyces cerevisiae Mus81-Mms4. Nucleic Acids Res 37: 2026–2036. doi: 10.1093/nar/gkp038
|
[61] | Fricke WM, Bastin-Shanower SA, Brill SJ (2005) Substrate specificity of the Saccharomyces cerevisiae Mus81-Mms4 endonuclease. DNA Repair (Amst) 4: 243–251. doi: 10.1016/j.dnarep.2004.10.001
|
[62] | Ohouo PY, Bastos de Oliveira FM, Almeida BS, Smolka MB (2010) DNA damage signaling recruits the Rtt107-Slx4 scaffolds via Dpb11 to mediate replication stress response. Mol Cell 39: 300–306. doi: 10.1016/j.molcel.2010.06.019
|
[63] | Roberts TM, Kobor MS, Bastin-Shanower SA, Ii M, Horte SA, et al. (2006) Slx4 regulates DNA damage checkpoint-dependent phosphorylation of the BRCT domain protein Rtt107/Esc4. Mol Biol Cell 17: 539–548. doi: 10.1091/mbc.e05-08-0785
|
[64] | De Muyt A, Jessop L, Kolar E, Sourirajan A, Chen J, et al. (2012) BLM helicase ortholog Sgs1 is a central regulator of meiotic recombination intermediate metabolism. Mol Cell 46: 43–53. doi: 10.1016/j.molcel.2012.02.020
|
[65] | Zakharyevich K, Tang S, Ma Y, Hunter N (2012) Delineation of joint molecule resolution pathways in meiosis identifies a crossover-specific resolvase. Cell 149: 334–347. doi: 10.1016/j.cell.2012.03.023
|
[66] | Ivanov EL, Haber JE (1995) RAD1 and RAD10, but not other excision repair genes, are required for double-strand break-induced recombination in Saccharomyces cerevisiae. Mol Cell Biol 15: 2245–2251.
|
[67] | Munoz-Galvan S, Tous C, Blanco MG, Schwartz EK, Ehmsen KT, et al. (2012) Distinct roles of mus81, yen1, slx1-slx4, and rad1 nucleases in the repair of replication-born double-strand breaks by sister chromatid exchange. Mol Cell Biol 32: 1592–1603. doi: 10.1128/mcb.00111-12
|
[68] | Rouse J (2009) Control of genome stability by SLX protein complexes. Biochem Soc Trans 37: 495–510. doi: 10.1042/bst0370495
|
[69] | Zhang F, Carvalho CM, Lupski JR (2009) Complex human chromosomal and genomic rearrangements. Trends Genet 25: 298–307. doi: 10.1016/j.tig.2009.05.005
|
[70] | Zou H, Rothstein R (1997) Holliday junctions accumulate in replication mutants via a RecA homolog-independent mechanism. Cell 90: 87–96. doi: 10.1016/s0092-8674(00)80316-5
|
[71] | Frank-Vaillant M, Marcand S (2001) NHEJ regulation by mating type is exercised through a novel protein, Lif2p, essential to the ligase IV pathway. Genes Dev 15: 3005–3012. doi: 10.1101/gad.206801
|