Nucleosome assembly and genome integrity

References

• Halazonetis TD, Gorgoulis VG, Bartek J. An oncogene-induced DNA damage model for cancer development. Science 2008; 319:1352 - 5; http://dx.doi.org/10.1126/science.1140735; PMID: 18323444
   PubMed Web of Science ®Google Scholar
• Tercero JA, Longhese MP, Diffley JFX. A central role for DNA replication forks in checkpoint activation and response. Mol Cell 2003; 11:1323 - 36; http://dx.doi.org/10.1016/S1097-2765(03)00169-2; PMID: 12769855
   PubMed Web of Science ®Google Scholar
• Kolodner RD, Putnam CD, Myung K. Maintenance of genome stability in Saccharomyces cerevisiae. Science 2002; 297:552 - 7; http://dx.doi.org/10.1126/science.1075277; PMID: 12142524
   PubMed Web of Science ®Google Scholar
• Ransom M, Dennehey BK, Tyler JK. Chaperoning histones during DNA replication and repair. Cell 2010; 140:183 - 95; http://dx.doi.org/10.1016/j.cell.2010.01.004; PMID: 20141833
   PubMed Web of Science ®Google Scholar
• Gunjan A, Verreault AA. A Rad53 kinase-dependent surveillance mechanism that regulates histone protein levels in S. cerevisiae. Cell 2003; 115:537 - 49; http://dx.doi.org/10.1016/S0092-8674(03)00896-1; PMID: 14651846
   PubMed Web of Science ®Google Scholar
• Groth A, Ray-Gallet D, Quivy J-P, Lukas J, Bartek J, Almouzni G. Human Asf1 regulates the flow of S phase histones during replicational stress. Mol Cell 2005; 17:301 - 11; http://dx.doi.org/10.1016/j.molcel.2004.12.018; PMID: 15664198
   PubMed Web of Science ®Google Scholar
• Groth A, Corpet A, Cook AJL, Roche D, Bartek J, Lukas J, et al. Regulation of replication fork progression through histone supply and demand. Science 2007; 318:1928 - 31; http://dx.doi.org/10.1126/science.1148992; PMID: 18096807
   PubMed Web of Science ®Google Scholar
• Prado F, Aguilera A. Partial depletion of histone H4 increases homologous recombination-mediated genetic instability. Mol Cell Biol 2005; 25:1526 - 36; http://dx.doi.org/10.1128/MCB.25.4.1526-1536.2005; PMID: 15684401
   PubMed Web of Science ®Google Scholar
• Prado F, Cortés-Ledesma F, Aguilera A. The absence of the yeast chromatin assembly factor Asf1 increases genomic instability and sister chromatid exchange. EMBO Rep 2004; 5:497 - 502; http://dx.doi.org/10.1038/sj.embor.7400128; PMID: 15071494
   PubMed Web of Science ®Google Scholar
• Burgess RJ, Zhou H, Han J, Zhang Z. A role for Gcn5 in replication-coupled nucleosome assembly. Mol Cell 2010; 37:469 - 80; http://dx.doi.org/10.1016/j.molcel.2010.01.020; PMID: 20188666
   PubMed Web of Science ®Google Scholar
• Han J, Zhou H, Horazdovsky B, Zhang K, Xu R-M, Zhang Z. Rtt109 acetylates histone H3 lysine 56 and functions in DNA replication. Science 2007; 315:653 - 5; http://dx.doi.org/10.1126/science.1133234; PMID: 17272723
   PubMed Web of Science ®Google Scholar
• Endo M, Ishikawa Y, Osakabe K, Nakayama S, Kaya H, Araki T, et al. Increased frequency of homologous recombination and T-DNA integration in Arabidopsis CAF-1 mutants. EMBO J 2006; 25:5579 - 90; http://dx.doi.org/10.1038/sj.emboj.7601434; PMID: 17110925
   PubMed Web of Science ®Google Scholar
• Driscoll R, Hudson A, Jackson SP. Yeast Rtt109 promotes genome stability by acetylating histone H3 on lysine 56. Science 2007; 315:649 - 52; http://dx.doi.org/10.1126/science.1135862; PMID: 17272722
   PubMed Web of Science ®Google Scholar
• Ye X, Franco AA, Santos H, Nelson DM, Kaufman PD, Adams PD. Defective S phase chromatin assembly causes DNA damage, activation of the S phase checkpoint, and S phase arrest. Mol Cell 2003; 11:341 - 51; http://dx.doi.org/10.1016/S1097-2765(03)00037-6; PMID: 12620223
   PubMed Web of Science ®Google Scholar
• Myung K, Pennaneach V, Kats ES, Kolodner RD. Saccharomyces cerevisiae chromatin-assembly factors that act during DNA replication function in the maintenance of genome stability. Proc Natl Acad Sci U S A 2003; 100:6640 - 5; http://dx.doi.org/10.1073/pnas.1232239100; PMID: 12750463
   PubMed Web of Science ®Google Scholar
• Li Q, Zhou H, Wurtele H, Davies B, Horazdovsky B, Verreault A, et al. Acetylation of histone H3 lysine 56 regulates replication-coupled nucleosome assembly. Cell 2008; 134:244 - 55; http://dx.doi.org/10.1016/j.cell.2008.06.018; PMID: 18662540
   PubMed Web of Science ®Google Scholar
• Masumoto H, Hawke D, Kobayashi R, Verreault A. A role for cell-cycle-regulated histone H3 lysine 56 acetylation in the DNA damage response. Nature 2005; 436:294 - 8; http://dx.doi.org/10.1038/nature03714; PMID: 16015338
   PubMed Web of Science ®Google Scholar
• Tsubota T, Berndsen CE, Erkmann JA, Smith CL, Yang L, Freitas MA, et al. Histone H3-K56 acetylation is catalyzed by histone chaperone-dependent complexes. Mol Cell 2007; 25:703 - 12; http://dx.doi.org/10.1016/j.molcel.2007.02.006; PMID: 17320445
   PubMed Web of Science ®Google Scholar
• Tyler JK, Adams CR, Chen S-R, Kobayashi R, Kamakaka RT, Kadonaga JT. The RCAF complex mediates chromatin assembly during DNA replication and repair. Nature 1999; 402:555 - 60; http://dx.doi.org/10.1038/990147; PMID: 10591219
   PubMed Web of Science ®Google Scholar
• Choy JS, Kron SJ. NuA4 subunit Yng2 function in intra-S-phase DNA damage response. Mol Cell Biol 2002; 22:8215 - 25; http://dx.doi.org/10.1128/MCB.22.23.8215-8225.2002; PMID: 12417725
   PubMed Web of Science ®Google Scholar
• Qin S, Parthun MR. Histone H3 and the histone acetyltransferase Hat1p contribute to DNA double-strand break repair. Mol Cell Biol 2002; 22:8353 - 65; http://dx.doi.org/10.1128/MCB.22.23.8353-8365.2002; PMID: 12417736
   PubMed Web of Science ®Google Scholar
• Clemente-Ruiz M, Prado F. Chromatin assembly controls replication fork stability. EMBO Rep 2009; 10:790 - 6; http://dx.doi.org/10.1038/embor.2009.67; PMID: 19465889
   PubMed Web of Science ®Google Scholar
• Clemente-Ruiz M, González-Prieto R, Prado F. Histone H3K56 acetylation, CAF1, and Rtt106 coordinate nucleosome assembly and stability of advancing replication forks. PLoS Genet 2011; 7:e1002376; http://dx.doi.org/10.1371/journal.pgen.1002376; PMID: 22102830
   PubMedGoogle Scholar
• Emili A, Schieltz DM, Yates JR 3rd, Hartwell LH. Dynamic interaction of DNA damage checkpoint protein Rad53 with chromatin assembly factor Asf1. Mol Cell 2001; 7:13 - 20; http://dx.doi.org/10.1016/S1097-2765(01)00150-2; PMID: 11172707
   PubMed Web of Science ®Google Scholar
• Hu F, Alcasabas AA, Elledge SJ. Asf1 links Rad53 to control of chromatin assembly. Genes Dev 2001; 15:1061 - 6; http://dx.doi.org/10.1101/gad.873201; PMID: 11331602
   PubMed Web of Science ®Google Scholar
• Ramey CJ, Howar S, Adkins M, Linger J, Spicer J, Tyler JK. Activation of the DNA damage checkpoint in yeast lacking the histone chaperone anti-silencing function 1. Mol Cell Biol 2004; 24:10313 - 27; http://dx.doi.org/10.1128/MCB.24.23.10313-10327.2004; PMID: 15542840
   PubMed Web of Science ®Google Scholar
• Kats ES, Albuquerque CP, Zhou H, Kolodner RD. Checkpoint functions are required for normal S-phase progression in Saccharomyces cerevisiae RCAF- and CAF-I-defective mutants. Proc Natl Acad Sci U S A 2006; 103:3710 - 5; http://dx.doi.org/10.1073/pnas.0511102103; PMID: 16501045
   PubMed Web of Science ®Google Scholar
• Franco AA, Lam WM, Burgers PM, Kaufman PD. Histone deposition protein Asf1 maintains DNA replisome integrity and interacts with replication factor C. Genes Dev 2005; 19:1365 - 75; http://dx.doi.org/10.1101/gad.1305005; PMID: 15901673
   PubMed Web of Science ®Google Scholar
• Han J, Zhou H, Li Z, Xu R-M, Zhang Z. Acetylation of lysine 56 of histone H3 catalyzed by RTT109 and regulated by ASF1 is required for replisome integrity. J Biol Chem 2007; 282:28587 - 96; http://dx.doi.org/10.1074/jbc.M702496200; PMID: 17690098
   PubMed Web of Science ®Google Scholar
• Collins SR, Miller KM, Maas NL, Roguev A, Fillingham J, Chu CS, et al. Functional dissection of protein complexes involved in yeast chromosome biology using a genetic interaction map. Nature 2007; 446:806 - 10; http://dx.doi.org/10.1038/nature05649; PMID: 17314980
   PubMed Web of Science ®Google Scholar
• Yang JH, Freudenreich CH. The Rtt109 histone acetyltransferase facilitates error-free replication to prevent CAG/CTG repeat contractions. DNA Repair (Amst) 2010; 9:414 - 20; http://dx.doi.org/10.1016/j.dnarep.2009.12.022; PMID: 20083442
   PubMed Web of Science ®Google Scholar
• Duro E, Vaisica JA, Brown GW, Rouse J. Budding yeast Mms22 and Mms1 regulate homologous recombination induced by replisome blockage. DNA Repair (Amst) 2008; 7:811 - 8; http://dx.doi.org/10.1016/j.dnarep.2008.01.007; PMID: 18321796
   PubMed Web of Science ®Google Scholar
• Wurtele H, Kaiser GS, Bacal J, St-Hilaire E, Lee E-H, Tsao S, et al. Histone H3 lysine 56 acetylation and the response to DNA replication fork damage. Mol Cell Biol 2012; 32:154 - 72; http://dx.doi.org/10.1128/MCB.05415-11; PMID: 22025679
   PubMed Web of Science ®Google Scholar
• Houseley J, Tollervey D. Repeat expansion in the budding yeast ribosomal DNA can occur independently of the canonical homologous recombination machinery. Nucleic Acids Res 2011; 39:8778 - 91; http://dx.doi.org/10.1093/nar/gkr589; PMID: 21768125
   PubMed Web of Science ®Google Scholar
• Erkmann JA, Kaufman PD. A negatively charged residue in place of histone H3K56 supports chromatin assembly factor association but not genotoxic stress resistance. DNA Repair (Amst) 2009; 8:1371 - 9; http://dx.doi.org/10.1016/j.dnarep.2009.09.004; PMID: 19796999
   PubMed Web of Science ®Google Scholar
• Roberts TM, Zaidi IW, Vaisica JA, Peter M, Brown GW. Regulation of rtt107 recruitment to stalled DNA replication forks by the cullin rtt101 and the rtt109 acetyltransferase. Mol Biol Cell 2008; 19:171 - 80; http://dx.doi.org/10.1091/mbc.E07-09-0961; PMID: 17978089
   PubMed Web of Science ®Google Scholar
• Zou H, Rothstein R. Holliday junctions accumulate in replication mutants via a RecA homolog-independent mechanism. Cell 1997; 90:87 - 96; http://dx.doi.org/10.1016/S0092-8674(00)80316-5; PMID: 9230305
   PubMed Web of Science ®Google Scholar
• Zheng L, Shen B. Okazaki fragment maturation: nucleases take centre stage. J Mol Cell Biol 2011; 3:23 - 30; http://dx.doi.org/10.1093/jmcb/mjq048; PMID: 21278448
   PubMed Web of Science ®Google Scholar
• Tishkoff DX, Filosi N, Gaida GM, Kolodner RD. A novel mutation avoidance mechanism dependent on S. cerevisiae RAD27 is distinct from DNA mismatch repair. Cell 1997; 88:253 - 63; http://dx.doi.org/10.1016/S0092-8674(00)81846-2; PMID: 9008166
   PubMed Web of Science ®Google Scholar
• Chen C, Kolodner RD. Gross chromosomal rearrangements in Saccharomyces cerevisiae replication and recombination defective mutants. Nat Genet 1999; 23:81 - 5; http://dx.doi.org/10.1038/12687; PMID: 10471504
   PubMed Web of Science ®Google Scholar
• Sogo JM, Stahl H, Koller T, Knippers R. Structure of replicating simian virus 40 minichromosomes. The replication fork, core histone segregation and terminal structures. J Mol Biol 1986; 189:189 - 204; http://dx.doi.org/10.1016/0022-2836(86)90390-6; PMID: 3023620
   PubMed Web of Science ®Google Scholar
• Lucchini R, Wellinger RE, Sogo JM. Nucleosome positioning at the replication fork. EMBO J 2001; 20:7294 - 302; http://dx.doi.org/10.1093/emboj/20.24.7294; PMID: 11743005
   PubMed Web of Science ®Google Scholar
• Cusick ME, Lee KS, DePamphilis ML, Wassarman PM. Structure of chromatin at deoxyribonucleic acid replication forks: nuclease hypersensitivity results from both prenucleosomal deoxyribonucleic acid and an immature chromatin structure. Biochemistry 1983; 22:3873 - 84; http://dx.doi.org/10.1021/bi00285a024; PMID: 6311255
   PubMed Web of Science ®Google Scholar
• Huggins CF, Chafin DR, Aoyagi S, Henricksen LA, Bambara RA, Hayes JJ. Flap endonuclease 1 efficiently cleaves base excision repair and DNA replication intermediates assembled into nucleosomes. Mol Cell 2002; 10:1201 - 11; http://dx.doi.org/10.1016/S1097-2765(02)00736-0; PMID: 12453426
   PubMed Web of Science ®Google Scholar
• Jagannathan I, Pepenella S, Hayes JJ. Activity of FEN1 endonuclease on nucleosome substrates is dependent upon DNA sequence but not flap orientation. J Biol Chem 2011; 286:17521 - 9; http://dx.doi.org/10.1074/jbc.M111.229658; PMID: 21454907
   PubMed Web of Science ®Google Scholar
• Corpet A, De Koning L, Toedling J, Savignoni A, Berger F, Lemaìtre C, et al. Asf1b, the necessary Asf1 isoform for proliferation, is predictive of outcome in breast cancer. EMBO J 2011; 30:480 - 93; http://dx.doi.org/10.1038/emboj.2010.335; PMID: 21179005
   PubMed Web of Science ®Google Scholar
• Feser J, Truong D, Das C, Carson JJ, Kieft J, Harkness T, et al. Elevated histone expression promotes life span extension. Mol Cell 2010; 39:724 - 35; http://dx.doi.org/10.1016/j.molcel.2010.08.015; PMID: 20832724
   PubMed Web of Science ®Google Scholar
• Smith DJ, Whitehouse I. Intrinsic coupling of lagging-strand synthesis to chromatin assembly. Nature 2012; 483:434 - 8; http://dx.doi.org/10.1038/nature10895; PMID: 22419157
   PubMed Web of Science ®Google Scholar