Sgs1 Helicase and Two Nucleases Dna2 and Exo1 Resect DNA Double-Strand Break Ends

Amundsen, 2003, Interchangeable parts of the Escherichia coli recombination machinery, Cell, 112, 741, 10.1016/S0092-8674(03)00197-1 Aravind, 2000, SURVEY AND SUMMARY: holliday junction resolvases and related nucleases: identification of new families, phyletic distribution and evolutionary trajectories, Nucleic Acids Res., 28, 3417, 10.1093/nar/28.18.3417 Bachrati, 2008, RecQ helicases: guardian angels of the DNA replication fork, Chromosoma, 117, 219, 10.1007/s00412-007-0142-4 Bae, 2001, RPA governs endonuclease switching during processing of Okazaki fragments in eukaryotes, Nature, 412, 456, 10.1038/35086609 Bae, 1998, Dna2 of Saccharomyces cerevisiae possesses a single-stranded DNA-specific endonuclease activity that is able to act on double-stranded DNA in the presence of ATP, J. Biol. Chem., 273, 26880, 10.1074/jbc.273.41.26880 Branzei, 2007, RecQ helicases queuing with Srs2 to disrupt Rad51 filaments and suppress recombination, Genes Dev., 21, 3019, 10.1101/gad.1624707 Budd, 1995, A yeast gene required for DNA replication encodes a protein with homology to DNA helicases, Proc. Natl. Acad. Sci. USA, 92, 7642, 10.1073/pnas.92.17.7642 Budd, 2000, The pattern of sensitivity of yeast dna2 mutants to DNA damaging agents suggests a role in DSB and postreplication repair pathways, Mutat. Res., 459, 173, 10.1016/S0921-8777(99)00072-5 Budd, 1995, DNA2 encodes a DNA helicase essential for replication of eukaryotic chromosomes, J. Biol. Chem., 270, 26766, 10.1074/jbc.270.45.26766 Budd, 2000, The nuclease activity of the yeast DNA2 protein, which is related to the RecB-like nucleases, is essential in vivo, J. Biol. Chem., 275, 16518, 10.1074/jbc.M909511199 Budd, 2006, Evidence suggesting that Pif1 helicase functions in DNA replication with the Dna2 helicase/nuclease and DNA polymerase delta, Mol. Cell. Biol., 26, 2490, 10.1128/MCB.26.7.2490-2500.2006 Chang, 2005, RMI1/NCE4, a suppressor of genome instability, encodes a member of the RecQ helicase/Topo III complex, EMBO J., 24, 2024, 10.1038/sj.emboj.7600684 Chen, 2007, Binding and activation of DNA topoisomerase III by the Rmi1 subunit, J. Biol. Chem., 282, 28971, 10.1074/jbc.M705427200 Chiolo, 2005, Srs2 and Sgs1 DNA helicases associate with Mre11 in different subcomplexes following checkpoint activation and CDK1-mediated Srs2 phosphorylation, Mol. Cell. Biol., 25, 5738, 10.1128/MCB.25.13.5738-5751.2005 Church, 1985, The genomic sequencing technique, Prog. Clin. Biol. Res., 177, 17 Clerici, 2005, The Saccharomyces cerevisiae Sae2 protein promotes resection and bridging of double strand break ends, J. Biol. Chem., 280, 38631, 10.1074/jbc.M508339200 Cotta-Ramusino, 2005, Exo1 processes stalled replication forks and counteracts fork reversal in checkpoint-defective cells, Mol. Cell, 17, 153, 10.1016/j.molcel.2004.11.032 Courcelle, 2006, Nascent DNA processing by RecJ favors lesion repair over translesion synthesis at arrested replication forks in Escherichia coli, Proc. Natl. Acad. Sci. USA, 103, 9154, 10.1073/pnas.0600785103 Davis, 2004, RAD51-dependent break-induced replication in yeast, Mol. Cell. Biol., 24, 2344, 10.1128/MCB.24.6.2344-2351.2004 Fishman-Lobell, 1992, Removal of nonhomologous DNA ends in double-strand break recombination: the role of the yeast ultraviolet repair gene RAD1, Science, 258, 480, 10.1126/science.1411547 Formosa, 1999, Dna2 mutants reveal interactions with Dna polymerase alpha and Ctf4, a Pol alpha accessory factor, and show that full Dna2 helicase activity is not essential for growth, Genetics, 151, 1459, 10.1093/genetics/151.4.1459 Fricke, 2001, Mapping the DNA topoisomerase III binding domain of the Sgs1 DNA helicase, J. Biol. Chem., 276, 8848, 10.1074/jbc.M009719200 Furuse, 1998, Distinct roles of two separable in vitro activities of yeast Mre11 in mitotic and meiotic recombination, EMBO J., 17, 6412, 10.1093/emboj/17.21.6412 Gangloff, 1994, The yeast type I topoisomerase Top3 interacts with Sgs1, a DNA helicase homolog: a potential eukaryotic reverse gyrase, Mol. Cell. Biol., 14, 8391 Harrison, 2006, Surviving the breakup: the DNA damage checkpoint, Annu. Rev. Genet., 40, 209, 10.1146/annurev.genet.40.051206.105231 Hishida, 2004, Role of the Escherichia coli RecQ DNA helicase in SOS signaling and genome stabilization at stalled replication forks, Genes Dev., 18, 1886, 10.1101/gad.1223804 Inbar, 1999, Homology search and choice of homologous partner during mitotic recombination, Mol. Cell. Biol., 19, 4134, 10.1128/MCB.19.6.4134 Ira, 2002, Characterization of RAD51-independent break-induced replication that acts preferentially with short homologous sequences, Mol. Cell. Biol., 22, 6384, 10.1128/MCB.22.18.6384-6392.2002 Ira, 2003, Srs2 and Sgs1-Top3 suppress crossovers during double-strand break repair in yeast, Cell, 115, 401, 10.1016/S0092-8674(03)00886-9 Ira, 2004, DNA end resection, homologous recombination and DNA damage checkpoint activation require CDK1, Nature, 431, 1011, 10.1038/nature02964 Ivanov, 1994, Mutations in XRS2 and RAD50 delay but do not prevent mating-type switching in Saccharomyces cerevisiae, Mol. Cell. Biol., 14, 3414 Jazayeri, 2006, ATM- and cell cycle-dependent regulation of ATR in response to DNA double-strand breaks, Nat. Cell Biol., 8, 37, 10.1038/ncb1337 Jinks-Robertson, 1993, Substrate length requirements for efficient mitotic recombination in Saccharomyces cerevisiae, Mol. Cell. Biol., 13, 3937 Kim, 2006, Isolation of human Dna2 endonuclease and characterization of its enzymatic properties, Nucleic Acids Res., 34, 1854, 10.1093/nar/gkl102 Lee, 2000, The endonuclease activity of the yeast Dna2 enzyme is essential in vivo, Nucleic Acids Res., 28, 2873, 10.1093/nar/28.15.2873 Lee, 1998, Saccharomyces Ku70, mre11/rad50 and RPA proteins regulate adaptation to G2/M arrest after DNA damage, Cell, 94, 399, 10.1016/S0092-8674(00)81482-8 Lee, 2002, Complementation between N-terminal Saccharomyces cerevisiae mre11 alleles in DNA repair and telomere length maintenance, DNA Repair (Amst.), 1, 27, 10.1016/S1568-7864(01)00003-9 Lengsfeld, 2007, Sae2 is an endonuclease that processes hairpin DNA cooperatively with the Mre11/Rad50/Xrs2 complex, Mol. Cell, 28, 638, 10.1016/j.molcel.2007.11.001 Lisby, 2004, Choreography of the DNA damage response: spatiotemporal relationships among checkpoint and repair proteins, Cell, 118, 699, 10.1016/j.cell.2004.08.015 Llorente, 2004, The Mre11 nuclease is not required for 5′ to 3′ resection at multiple HO-induced double-strand breaks, Mol. Cell. Biol., 24, 9682, 10.1128/MCB.24.21.9682-9694.2004 Magner, 2007, RecQ promotes toxic recombination in cells lacking recombination intermediate-removal proteins, Mol. Cell, 26, 273, 10.1016/j.molcel.2007.03.012 Maringele, 2002, EXO1-dependent single-stranded DNA at telomeres activates subsets of DNA damage and spindle checkpoint pathways in budding yeast yku70Delta mutants, Genes Dev., 16, 1919, 10.1101/gad.225102 Masuda-Sasa, 2006, Biochemical analysis of human Dna2, Nucleic Acids Res., 34, 1865, 10.1093/nar/gkl070 Melo, 2001, Two checkpoint complexes are independently recruited to sites of DNA damage in vivo, Genes Dev., 15, 2809, 10.1101/gad.903501 Mnaimneh, 2004, Exploration of essential gene functions via titratable promoter alleles, Cell, 118, 31, 10.1016/j.cell.2004.06.013 Moreau, 1999, The nuclease activity of Mre11 is required for meiosis but not for mating type switching, end joining, or telomere maintenance, Mol. Cell. Biol., 19, 556, 10.1128/MCB.19.1.556 Mullen, 2005, Yeast Rmi1/Nce4 controls genome stability as a subunit of the Sgs1-Top3 complex, Mol. Cell. Biol., 25, 4476, 10.1128/MCB.25.11.4476-4487.2005 Myung, 2001, SGS1, the Saccharomyces cerevisiae homologue of BLM and WRN, suppresses genome instability and homeologous recombination, Nat. Genet., 27, 113, 10.1038/83673 Neale, 2005, Endonucleolytic processing of covalent protein-linked DNA double-strand breaks, Nature, 436, 1053, 10.1038/nature03872 Paull, 1998, The 3′ to 5′ exonuclease activity of Mre 11 facilitates repair of DNA double-strand breaks, Mol. Cell, 1, 969, 10.1016/S1097-2765(00)80097-0 Raynard, 2006, A double Holliday junction dissolvasome comprising BLM, topoisomerase IIIalpha, and BLAP75, J. Biol. Chem., 281, 13861, 10.1074/jbc.C600051200 San Filippo, 2008, Mechanism of eukaryotic homologous recombination, Annu. Rev. Biochem., 77, 229, 10.1146/annurev.biochem.77.061306.125255 Sartori, 2007, Human CtIP promotes DNA end resection, Nature, 450, 509, 10.1038/nature06337 Schulz, 1994, The saccharomyces PIF1 DNA helicase inhibits telomere elongation and de novo telomere formation, Cell, 76, 145, 10.1016/0092-8674(94)90179-1 Shim, 2007, RSC mobilizes nucleosomes to improve accessibility of repair machinery to the damaged chromatin, Mol. Cell. Biol., 27, 1602, 10.1128/MCB.01956-06 Shroff, 2004, Distribution and dynamics of chromatin modification induced by a defined DNA double-strand break, Curr. Biol., 14, 1703, 10.1016/j.cub.2004.09.047 Spies, 2005, Homologous recombination by RecBCD and RecF pathways, 389 Sun, 1991, Extensive 3′-overhanging, single-stranded DNA associated with the meiosis-specific double-strand breaks at the ARG4 recombination initiation site, Cell, 64, 1155, 10.1016/0092-8674(91)90270-9 Symington, 2002, Role of RAD52 epistasis group genes in homologous recombination and double-strand break repair, Microbiol. Mol. Biol. Rev., 66, 630, 10.1128/MMBR.66.4.630-670.2002 Toczylowski, 2006, Mechanistic analysis of a DNA end processing pathway mediated by the Xenopus Werner syndrome protein, J. Biol. Chem., 281, 33198, 10.1074/jbc.M605044200 Trujillo, 1998, Nuclease activities in a complex of human recombination and DNA repair factors Rad50, Mre11, and p95, J. Biol. Chem., 273, 21447, 10.1074/jbc.273.34.21447 Tsubouchi, 1998, A novel mre11 mutation impairs processing of double-strand breaks of DNA during both mitosis and meiosis, Mol. Cell. Biol., 18, 260, 10.1128/MCB.18.1.260 Tsubouchi, 2000, Exo1 roles for repair of DNA double-strand breaks and meiotic crossing over in Saccharomyces cerevisiae, Mol. Biol. Cell, 11, 2221, 10.1091/mbc.11.7.2221 Usui, 1998, Complex formation and functional versatility of Mre11 of budding yeast in recombination, Cell, 95, 705, 10.1016/S0092-8674(00)81640-2 van Attikum, 2004, Recruitment of the INO80 complex by H2A phosphorylation links ATP-dependent chromatin remodeling with DNA double-strand break repair, Cell, 119, 777, 10.1016/j.cell.2004.11.033 VanHulle, 2007, Inverted DNA repeats channel repair of distant double-strand breaks into chromatid fusions and chromosomal rearrangements, Mol. Cell. Biol., 27, 2601, 10.1128/MCB.01740-06 Vaze, 2002, Recovery from checkpoint-mediated arrest after repair of a double-strand break requires srs2 helicase, Mol. Cell, 10, 373, 10.1016/S1097-2765(02)00593-2 Watt, 1996, SGS1, a homologue of the Bloom's and Werner's syndrome genes, is required for maintenance of genome stability in Saccharomyces cerevisiae, Genetics, 144, 935, 10.1093/genetics/144.3.935 White, 1990, Intermediates of recombination during mating type switching in Saccharomyces cerevisiae, EMBO J., 9, 663, 10.1002/j.1460-2075.1990.tb08158.x Wu, 2003, The Bloom's syndrome helicase suppresses crossing over during homologous recombination, Nature, 426, 870, 10.1038/nature02253 Wu, 2000, The Bloom's syndrome gene product interacts with topoisomerase III, J. Biol. Chem., 275, 9636, 10.1074/jbc.275.13.9636 Yin, 2005, BLAP75, an essential component of Bloom's syndrome protein complexes that maintain genome integrity, EMBO J., 24, 1465, 10.1038/sj.emboj.7600622 Zeng, 2006, In vivo dual cross-linking for identification of indirect DNA-associated proteins by chromatin immunoprecipitation, Biotechniques, 41, 10.2144/000112297 Zhou, 2000, Pif1p helicase, a catalytic inhibitor of telomerase in yeast, Science, 289, 771, 10.1126/science.289.5480.771 Zou, 2003, Sensing DNA damage through ATRIP recognition of RPA-ssDNA complexes, Science, 300, 1542, 10.1126/science.1083430