Chromatin Challenges during DNA Replication and Repair

Aagaard, 1999, Functional mammalian homologues of the Drosophila PEV-modifier Su(var)3–9 encode centromere-associated proteins which complex with the heterochromatin component M31, EMBO J., 18, 1923, 10.1093/emboj/18.7.1923 Ahmad, 2002, The histone variant H3.3 marks active chromatin by replication-independent nucleosome assembly, Mol. Cell, 9, 1191, 10.1016/S1097-2765(02)00542-7 Annunziato, 1983, Histone deacetylation is required for the maturation of newly replicated chromatin, J. Biol. Chem., 258, 12675, 10.1016/S0021-9258(17)44229-3 Barman, 2006, Histone acetyltransferase 1 is dispensable for replication-coupled chromatin assembly but contributes to recover DNA damages created following replication blockage in vertebrate cells, Biochem. Biophys. Res. Commun., 345, 1547, 10.1016/j.bbrc.2006.05.079 Belotserkovskaya, 2004, Facts about FACT and transcript elongation through chromatin, Curr. Opin. Genet. Dev., 14, 139, 10.1016/j.gde.2004.02.004 Benson, 2006, Modifications of H3 and H4 during chromatin replication, nucleosome assembly, and histone exchange, J. Biol. Chem., 281, 9287, 10.1074/jbc.M512956200 Bird, 2002, Acetylation of histone H4 by Esa1 is required for DNA double-strand break repair, Nature, 419, 411, 10.1038/nature01035 Celic, 2006, The sirtuins hst3 and Hst4p preserve genome integrity by controlling histone h3 lysine 56 deacetylation, Curr. Biol., 16, 1280, 10.1016/j.cub.2006.06.023 Chuang, 1997, Human DNA-(cytosine-5) methyltransferase-PCNA complex as a target for p21WAF1, Science, 277, 1996, 10.1126/science.277.5334.1996 Collins, 2002, An ACF1-ISWI chromatin-remodeling complex is required for DNA replication through heterochromatin, Nat. Genet., 32, 627, 10.1038/ng1046 Davey, 2002, Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 a resolution, J. Mol. Biol., 319, 1097, 10.1016/S0022-2836(02)00386-8 Dokmanovic, 2005, Prospects: histone deacetylase inhibitors, J. Cell. Biochem., 96, 293, 10.1002/jcb.20532 Downs, 2004, Binding of chromatin-modifying activities to phosphorylated histone H2A at DNA damage sites, Mol. Cell, 16, 979, 10.1016/j.molcel.2004.12.003 Ekwall, 1997, Transient inhibition of histone deacetylation alters the structural and functional imprint at fission yeast centromeres, Cell, 91, 1021, 10.1016/S0092-8674(00)80492-4 English, 2005, ASF1 binds to a heterodimer of histones H3 and H4: a two-step mechanism for the assembly of the H3–H4 heterotetramer on DNA, Biochemistry, 44, 13673, 10.1021/bi051333h English, 2006, Structural basis for the histone chaperone activity of asf1, Cell, 127, 495, 10.1016/j.cell.2006.08.047 Esteve, 2006, Direct interaction between DNMT1and G9a coordinates DNA and histone methylation during replication, Genes Dev., 20, 3089, 10.1101/gad.1463706 Feldman, 2006, G9a-mediated irreversible epigenetic inactivation of Oct-3/4 during early embryogenesis, Nat. Cell Biol., 8, 188, 10.1038/ncb1353 Fisher, 2003, Vertebrate HoxB gene expression requires DNA replication, EMBO J., 22, 3737, 10.1093/emboj/cdg352 Forlani, 1998, Relief of a repressed gene expression state in the mouse 1-cell embryo requires DNA replication, Development, 125, 3153, 10.1242/dev.125.16.3153 Formosa, 2003, Changing the DNA landscape: putting a SPN on chromatin, Curr. Top. Microbiol. Immunol., 274, 171 Fujita, 2003, Methyl-CpG binding domain 1 (MBD1) interacts with the Suv39h1–HP1 heterochromatic complex for DNA methylation-based transcriptional repression, J. Biol. Chem., 278, 24132, 10.1074/jbc.M302283200 Fuks, 2000, DNA methyltransferase Dnmt1 associates with histone deacetylase activity, Nat. Genet., 24, 88, 10.1038/71750 Fyodorov, 2004, Acf1 confers unique activities to ACF/CHRAC and promotes the formation rather than disruption of chromatin in vivo, Genes Dev., 18, 170, 10.1101/gad.1139604 Gaillard, 1996, Chromatin assembly coupled to DNA repair: a new role for chromatin assembly factor I, Cell, 86, 887, 10.1016/S0092-8674(00)80164-6 Gambus, 2006, GINS maintains association of Cdc45 with MCM in replisome progression complexes at eukaryotic DNA replication forks, Nat. Cell Biol., 8, 358, 10.1038/ncb1382 Gerard, 2006, The replication kinase Cdc7-Dbf4 promotes the interaction of the p150 subunit of chromatin assembly factor 1 with proliferating cell nuclear antigen, EMBO Rep., 7, 817, 10.1038/sj.embor.7400750 Glowczewski, 2004, Yeast chromatin assembly complex 1 protein excludes nonacetylatable forms of histone H4 from chromatin and the nucleus, Mol. Cell. Biol., 24, 10180, 10.1128/MCB.24.23.10180-10192.2004 Green, 2002, When repair meets chromatin. First in series on chromatin dynamics, EMBO Rep., 3, 28, 10.1093/embo-reports/kvf005 Green, 2003, Local action of the chromatin assembly factor CAF-1 at sites of nucleotide excision repair in vivo, EMBO J., 22, 5163, 10.1093/emboj/cdg478 Groth, 2003, Human Tousled like kinases are targeted by an ATM- and Chk1-dependent DNA damage checkpoint, EMBO J., 22, 1676, 10.1093/emboj/cdg151 Groth, 2005, Human Asf1 regulates the flow of S phase histones during replicational stress, Mol. Cell, 17, 301, 10.1016/j.molcel.2004.12.018 Gruss, 1993, Disruption of the nucleosomes at the replication fork, EMBO J., 12, 4533, 10.1002/j.1460-2075.1993.tb06142.x Gunjan, 2003, A Rad53 kinase-dependent surveillance mechanism that regulates histone protein levels in S. cerevisiae, Cell, 115, 537, 10.1016/S0092-8674(03)00896-1 Houlard, 2006, CAF-1 is essential for heterochromatin organization in pluripotent embryonic cells, PLoS Genet., 2, e181, 10.1371/journal.pgen.0020181 Huyen, 2004, Methylated lysine 79 of histone H3 targets 53BP1 to DNA double-strand breaks, Nature, 432, 406, 10.1038/nature03114 Jackson, 1988, Deposition of newly synthesized histones: hybrid nucleosomes are not tandemly arranged on daughter DNA strands, Biochemistry, 27, 2109, 10.1021/bi00406a044 Keogh, 2006, A phosphatase complex that dephosphorylates gammaH2AX regulates DNA damage checkpoint recovery, Nature, 439, 497, 10.1038/nature04384 Kim, 1988, Effects of histone H4 depletion on the cell cycle and transcription of Saccharomyces cerevisiae, EMBO J., 7, 2211, 10.1002/j.1460-2075.1988.tb03060.x Kimura, 2001, Kinetics of core histones in living human cells: little exchange of H3 and H4 and some rapid exchange of H2B, J. Cell Biol., 153, 1341, 10.1083/jcb.153.7.1341 Kouskouti, 2005, Histone modifications defining active genes persist after transcriptional and mitotic inactivation, EMBO J., 24, 347, 10.1038/sj.emboj.7600516 Krause, 2003, Suppression of Tousled-like kinase activity after DNA damage or replication block requires ATM, NBS1 and Chk1, Oncogene, 22, 5927, 10.1038/sj.onc.1206691 Krude, 1995, Chromatin assembly factor 1 (CAF-1) colocalizes with replication foci in HeLa cell nuclei, Exp. Cell Res., 220, 304, 10.1006/excr.1995.1320 Kusch, 2004, Acetylation by Tip60 is required for selective histone variant exchange at DNA lesions, Science, 306, 2084, 10.1126/science.1103455 Lan, 2004, In situ analysis of repair processes for oxidative DNA damage in mammalian cells, Proc. Natl. Acad. Sci. USA, 101, 13738, 10.1073/pnas.0406048101 Leonhardt, 1992, A targeting sequence directs DNA methyltransferase to sites of DNA replication in mammalian nuclei, Cell, 71, 865, 10.1016/0092-8674(92)90561-P Little, 2003, Genomic instability and bystander effects: a historical perspective, Oncogene, 22, 6978, 10.1038/sj.onc.1206988 Loyola, 2006, PTMs on H3 variants before chromatin assembly potentiate their final epigenetic state, Mol. Cell, 24, 309, 10.1016/j.molcel.2006.08.019 Ma, 1998, Deposition-related sites K5/K12 in histone H4 are not required for nucleosome deposition in yeast, Proc. Natl. Acad. Sci. USA, 95, 6693, 10.1073/pnas.95.12.6693 Maas, 2006, Cell cycle and checkpoint regulation of histone H3 K56 acetylation by Hst3 and Hst4, Mol. Cell, 23, 109, 10.1016/j.molcel.2006.06.006 Maison, 2004, HP1 and the dynamics of heterochromatin maintenance, Nat. Rev. Mol. Cell Biol., 5, 296, 10.1038/nrm1355 Martin, 1999, Relocalization of telomeric Ku and SIR proteins in response to DNA strand breaks in yeast, Cell, 97, 621, 10.1016/S0092-8674(00)80773-4 Masumoto, 2005, A role for cell-cycle-regulated histone H3 lysine 56 acetylation in the DNA damage response, Nature, 436, 294, 10.1038/nature03714 McAinsh, 1999, DNA damage triggers disruption of telomeric silencing and Mec1p-dependent relocation of Sir3p, Curr. Biol., 9, 963, 10.1016/S0960-9822(99)80424-2 Mello, 2002, Human Asf1 and CAF-1 interact and synergize in a repair-coupled nucleosome assembly pathway, EMBO Rep., 3, 329, 10.1093/embo-reports/kvf068 Mills, 1999, MEC1-dependent redistribution of the Sir3 silencing protein from telomeres to DNA double-strand breaks, Cell, 97, 609, 10.1016/S0092-8674(00)80772-2 Milutinovic, 2002, Proliferating cell nuclear antigen associates with histone deacetylase activity, integrating DNA replication and chromatin modification, J. Biol. Chem., 277, 20974, 10.1074/jbc.M202504200 Moggs, 2000, A CAF-1-PCNA-mediated chromatin assembly pathway triggered by sensing DNA damage, Mol. Cell. Biol., 20, 1206, 10.1128/MCB.20.4.1206-1218.2000 Morrison, 2004, INO80 and gamma-H2AX interaction links ATP-dependent chromatin remodeling to DNA damage repair, Cell, 119, 767, 10.1016/j.cell.2004.11.037 Mortusewicz, 2005, Recruitment of DNA methyltransferase I to DNA repair sites, Proc. Natl. Acad. Sci. USA, 102, 8905, 10.1073/pnas.0501034102 Mosammaparast, 2002, Pathways mediating the nuclear import of histones H3 and H4 in yeast, J. Biol. Chem., 277, 862, 10.1074/jbc.M106845200 Mousson, 2005, Structural basis for the interaction of Asf1 with histone H3 and its functional implications, Proc. Natl. Acad. Sci. USA, 102, 5975, 10.1073/pnas.0500149102 Mousson, 2006, The histone chaperone Asf1 at the crossroads of chromatin and DNA checkpoint pathways, Chromosoma Murr, 2006, Histone acetylation by Trrap-Tip60 modulates loading of repair proteins and repair of DNA double-strand breaks, Nat. Cell Biol., 8, 91, 10.1038/ncb1343 Murzina, 1999, Heterochromatin dynamics in mouse cells: interaction between chromatin assembly factor 1 and HP1 proteins, Mol. Cell, 4, 529, 10.1016/S1097-2765(00)80204-X Myung, 2003, Saccharomyces cerevisiae chromatin-assembly factors that act during DNA replication function in the maintenance of genome stability, Proc. Natl. Acad. Sci. USA, 100, 6640, 10.1073/pnas.1232239100 Nabatiyan, 2006, Induction of CAF-1 expression in response to DNA strand breaks in quiescent human cells, Mol. Cell. Biol., 26, 1839, 10.1128/MCB.26.5.1839-1849.2006 Okuwaki, 2004, Maintenance DNA methylation of nucleosome core particles, J. Biol. Chem., 279, 2904, 10.1074/jbc.M310111200 Papamichos-Chronakis, 2006, Interplay between Ino80 and Swr1 chromatin remodeling enzymes regulates cell cycle checkpoint adaptation in response to DNA damage, Genes Dev., 20, 2437, 10.1101/gad.1440206 Peters, 2001, Loss of the Suv39h histone methyltransferases impairs mammalian heterochromatin and genome stability, Cell, 107, 323, 10.1016/S0092-8674(01)00542-6 Peterson, 2004, Cellular machineries for chromosomal DNA repair, Genes Dev., 18, 602, 10.1101/gad.1182704 Polo, 2006, Chromatin assembly: a basic recipe with various flavours, Curr. Opin. Genet. Dev., 16, 104, 10.1016/j.gde.2006.02.011 Polo, 2006, New histone incorporation marks sites of UV repair in human cells, Cell, 127, 481, 10.1016/j.cell.2006.08.049 Poot, 2004, The Williams syndrome transcription factor interacts with PCNA to target chromatin remodelling by ISWI to replication foci, Nat. Cell Biol., 6, 1236, 10.1038/ncb1196 Prior, 1980, Incorporation of exogenous pyrene-labeled histone into Physarum chromatin: a system for studying changes in nucleosomes assembled in vivo, Cell, 20, 597, 10.1016/0092-8674(80)90306-2 Quivy, 2001, Dimerization of the largest subunit of chromatin assembly factor 1: importance in vitro and during Xenopus early development, EMBO J., 20, 2015, 10.1093/emboj/20.8.2015 Quivy, 2004, A CAF-1 dependent pool of HP1 during heterochromatin duplication, EMBO J., 23, 3516, 10.1038/sj.emboj.7600362 Randall, 1992, The fate of parental nucleosomes during SV40 DNA replication, J. Biol. Chem., 267, 14259, 10.1016/S0021-9258(19)49706-8 Recht, 2006, Histone chaperone Asf1 is required for histone H3 lysine 56 acetylation, a modification associated with S phase in mitosis and meiosis, Proc. Natl. Acad. Sci. USA, 103, 6988, 10.1073/pnas.0601676103 Reese, 2003, The methyl-CpG binding protein MBD1 interacts with the p150 subunit of chromatin assembly factor 1, Mol. Cell. Biol., 23, 3226, 10.1128/MCB.23.9.3226-3236.2003 Robertson, 2004, Effects of chromatin structure on the enzymatic and DNA binding functions of DNA methyltransferases DNMT1 and Dnmt3a in vitro, Biochem. Biophys. Res. Commun., 322, 110, 10.1016/j.bbrc.2004.07.083 Rountree, 2000, DNMT1 binds HDAC2 and a new co-repressor, DMAP1, to form a complex at replication foci, Nat. Genet., 25, 269, 10.1038/77023 Sanders, 2004, Methylation of histone H4 lysine 20 controls recruitment of Crb2 to sites of DNA damage, Cell, 119, 603, 10.1016/j.cell.2004.11.009 Sarraf, 2004, Methyl-CpG binding protein MBD1 couples histone H3 methylation at lysine 9 by SETDB1 to DNA replication and chromatin assembly, Mol. Cell, 15, 595, 10.1016/j.molcel.2004.06.043 Shibahara, 1999, Replication-dependent marking of DNA by PCNA facilitates CAF-1-coupled inheritance of chromatin, Cell, 96, 575, 10.1016/S0092-8674(00)80661-3 Shogren-Knaak, 2006, Histone H4–K16 acetylation controls chromatin structure and protein interactions, Science, 311, 844, 10.1126/science.1124000 Smerdon, 1991, DNA repair and the role of chromatin structure, Curr. Opin. Cell Biol., 3, 422, 10.1016/0955-0674(91)90069-B Sobel, 1995, Conservation of deposition-related acetylation sites in newly synthesized histones H3 and H4, Proc. Natl. Acad. Sci. USA, 92, 1237, 10.1073/pnas.92.4.1237 Sogo, 1986, Structure of replicating simian virus 40 minichromosomes. The replication fork, core histone segregation and terminal structures, J. Mol. Biol., 189, 189, 10.1016/0022-2836(86)90390-6 Sporbert, 2002, DNA polymerase clamp shows little turnover at established replication sites but sequential de novo assembly at adjacent origin clusters, Mol. Cell, 10, 1355, 10.1016/S1097-2765(02)00729-3 Strom, 2004, Postreplicative recruitment of cohesin to double-strand breaks is required for DNA repair, Mol. Cell, 16, 1003, 10.1016/j.molcel.2004.11.026 Taddei, 1999, Duplication and maintenance of heterochromatin domains, J. Cell Biol., 147, 1153, 10.1083/jcb.147.6.1153 Taddei, 2001, Reversible disruption of pericentric heterochromatin and centromere function by inhibiting deacetylases, Nat. Cell Biol., 3, 114, 10.1038/35055010 Tagami, 2004, Histone H3.1 and H3.3 complexes mediate nucleosome assembly pathways dependent or independent of DNA synthesis, Cell, 116, 51, 10.1016/S0092-8674(03)01064-X Takahashi, 2005, Pumps, paradoxes and ploughshares: mechanism of the MCM2–7 DNA helicase, Trends Biochem. Sci., 30, 437, 10.1016/j.tibs.2005.06.007 Tamburini, 2005, Localized histone acetylation and deacetylation triggered by the homologous recombination pathway of double-strand DNA repair, Mol. Cell. Biol., 25, 4903, 10.1128/MCB.25.12.4903-4913.2005 Tan, 2006, Functional cooperation between FACT and MCM helicase facilitates initiation of chromatin DNA replication, EMBO J., 25, 3975, 10.1038/sj.emboj.7601271 Tsukuda, 2005, Chromatin remodelling at a DNA double-strand break site in Saccharomyces cerevisiae, Nature, 438, 379, 10.1038/nature04148 Tyler, 1999, The RCAF complex mediates chromatin assembly during DNA replication and repair, Nature, 402, 555, 10.1038/990147 Unal, 2004, DNA damage response pathway uses histone modification to assemble a double-strand break-specific cohesin domain, Mol. Cell, 16, 991, 10.1016/j.molcel.2004.11.027 van Attikum, 2005, The histone code at DNA breaks: a guide to repair?, Nat. Rev. Mol. Cell Biol., 6, 757, 10.1038/nrm1737 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 van Leeuwen, 2002, Dot1p modulates silencing in yeast by methylation of the nucleosome core, Cell, 109, 745, 10.1016/S0092-8674(02)00759-6 Vire, 2006, The Polycomb group protein EZH2 directly controls DNA methylation, Nature, 439, 871, 10.1038/nature04431 Volkel, 2007, The control of histone lysine methylation in epigenetic regulation, Biochimie, 89, 1, 10.1016/j.biochi.2006.07.009 Wallace, 2005, Replication of heterochromatin: insights into mechanisms of epigenetic inheritance, Chromosoma, 114, 389, 10.1007/s00412-005-0024-6 Wang, 2006, Histone H3 and H4 ubiquitylation by the CUL4-DDB-ROC1 ubiquitin ligase facilitates cellular response to DNA damage, Mol. Cell, 22, 383, 10.1016/j.molcel.2006.03.035 Wurtele, 2006, Histone post-translational modifications and the response to DNA double-strand breaks, Curr. Opin. Cell Biol., 18, 137, 10.1016/j.ceb.2006.02.008 Ye, 2005, Histone H4 lysine 91 acetylation a core domain modification associated with chromatin assembly, Mol. Cell, 18, 123, 10.1016/j.molcel.2005.02.031 Yu, 2005, UV irradiation stimulates histone acetylation and chromatin remodeling at a repressed yeast locus, Proc. Natl. Acad. Sci. USA, 102, 8650, 10.1073/pnas.0501458102 Zhang, 2000, PCNA connects DNA replication to epigenetic inheritance in yeast, Nature, 408, 221, 10.1038/35048530 Zhou, 2006, Chromatin assembly factor 1 interacts with histone H3 methylated at lysine 79 in the processes of epigenetic silencing and DNA repair, Biochemistry, 45, 2852, 10.1021/bi0521083