Chromatin dynamics and the repair of DNA double strand breaks

References

• Huertas P. DNA resection in eukaryotes: deciding how to fix the break. Nat Struct Mol Biol 2010; 17:11 - 16
   PubMed Web of Science ®Google Scholar
• Jackson SP, Bartek J. The DNA-damage response in human biology and disease. Nature 2009; 461:1071 - 1078
   PubMed Web of Science ®Google Scholar
• Bonner WM, Redon CE, Dickey JS, Nakamura AJ, Sedelnikova OA, Solier S, et al. GammaH2AX and cancer. Nat Rev Cancer 2008; 8:957 - 967
   PubMed Web of Science ®Google Scholar
• Stucki M, Clapperton JA, Mohammad D, Yaffe MB, Smerdon SJ, Jackson SP. MDC1 directly binds phosphorylated histone H2AX to regulate cellular responses to DNA double-strand breaks. Cell 2005; 123:1213 - 1226
   PubMed Web of Science ®Google Scholar
• Melander F, Bekker-Jensen S, Falck J, Bartek J, Mailand N, Lukas J. Phosphorylation of SDT repeats in the MDC1 N terminus triggers retention of NBS1 at the DNA damage-modified chromatin. J Cell Biol 2008; 181:213 - 226
   PubMed Web of Science ®Google Scholar
• Spycher C, Miller ES, Townsend K, Pavic L, Morrice NA, Janscak P, et al. Constitutive phosphorylation of MDC1 physically links the MRE11-RAD50-NBS1 complex to damaged chromatin. J Cell Biol 2008; 181:227 - 240
   PubMed Web of Science ®Google Scholar
• Kolas NK, Chapman JR, Nakada S, Ylanko J, Chahwan R, Sweeney FD, et al. Orchestration of the DNA-damage response by the RNF8 ubiquitin ligase. Science 2007; 318:1637 - 1640
   PubMed Web of Science ®Google Scholar
• Campos EI, Reinberg D. Histones: annotating chromatin. Annu Rev Genet 2009; 43:559 - 599
   PubMed Web of Science ®Google Scholar
• Groth A, Rocha W, Verreault A, Almouzni G. Chromatin challenges during DNA replication and repair. Cell 2007; 128:721 - 733
   PubMed Web of Science ®Google Scholar
• Barski A, Cuddapah S, Cui K, Roh TY, Schones DE, Wang Z, et al. High-resolution profiling of histone methylations in the human genome. Cell 2007; 129:823 - 837
   PubMed Web of Science ®Google Scholar
• Guenther MG, Levine SS, Boyer LA, Jaenisch R, Young RA. A chromatin landmark and transcription initiation at most promoters in human cells. Cell 2007; 130:77 - 88
   PubMed Web of Science ®Google Scholar
• de Wit E, van Steensel B. Chromatin domains in higher eukaryotes: insights from genome-wide mapping studies. Chromosoma 2009; 118:25 - 36
   PubMed Web of Science ®Google Scholar
• Peng JC, Karpen GH. Epigenetic regulation of heterochromatic DNA stability. Curr Opin Genet Dev 2008; 18:204 - 211
   PubMed Web of Science ®Google Scholar
• Vakoc CR, Sachdeva MM, Wang H, Blobel GA. Profile of histone lysine methylation across transcribed mammalian chromatin. Mol Cell Biol 2006; 26:9185 - 9195
   PubMed Web of Science ®Google Scholar
• Pokholok DK, Harbison CT, Levine S, Cole M, Hannett NM, Lee TI, et al. Genome-wide map of nucleosome acetylation and methylation in yeast. Cell 2005; 122:517 - 527
   PubMed Web of Science ®Google Scholar
• Clapier CR, Cairns BR. The biology of chromatin remodeling complexes. Annu Rev Biochem 2009; 78:273 - 304
   PubMed Web of Science ®Google Scholar
• Cairns BR. Chromatin remodeling complexes: strength in diversity, precision through specialization. Curr Opin Genet Dev 2005; 15:185 - 190
   PubMed Web of Science ®Google Scholar
• Tsukuda T, Fleming AB, Nickoloff JA, Osley MA. Chromatin remodelling at a DNA double-strand break site in Saccharomyces cerevisiae. Nature 2005; 438:379 - 383
   PubMed Web of Science ®Google Scholar
• Shroff R, Arbel-Eden A, Pilch D, Ira G, Bonner WM, Petrini JH, et al. Distribution and dynamics of chromatin modification induced by a defined DNA double-strand break. Curr Biol 2004; 14:1703 - 1711
   PubMed Web of Science ®Google Scholar
• Berkovich E, Monnat RJ Jr, Kastan MB. Roles of ATM and NBS1 in chromatin structure modulation and DNA double-strand break repair. Nat Cell Biol 2007; 9:683 - 690
   PubMed Web of Science ®Google Scholar
• Lavin MF. ATM and the Mre11 complex combine to recognize and signal DNA double-strand breaks. Oncogene 2007; 26:7749 - 7758
   PubMed Web of Science ®Google Scholar
• Sinha M, Peterson CL. Chromatin dynamics during repair of chromosomal DNA double-strand breaks. Epigenomics 2009; 1:371 - 385
   PubMed Web of Science ®Google Scholar
• Rubbi CP, Milner J. p53 is a chromatin accessibility factor for nucleotide excision repair of DNA damage. EMBO J 2003; 22:975 - 986
   PubMed Web of Science ®Google Scholar
• Carrier F, Georgel PT, Pourquier P, Blake M, Kontny HU, Antinore MJ, et al. Gadd45, a p53-responsive stress protein, modifies DNA accessibility on damaged chromatin. Mol Cell Biol 1999; 19:1673 - 1685
   PubMed Web of Science ®Google Scholar
• Ziv Y, Bielopolski D, Galanty Y, Lukas C, Taya Y, Schultz DC, et al. Chromatin relaxation in response to DNA double-strand breaks is modulated by a novel ATM- and KAP-1 dependent pathway. Nat Cell Biol 2006; 8:870 - 876
   PubMed Web of Science ®Google Scholar
• Telford DJ, Stewart BW. Micrococcal nuclease: its specificity and use for chromatin analysis. Int J Biochem 1989; 21:127 - 137
   PubMedGoogle Scholar
• Goodarzi AA, Noon AT, Deckbar D, Ziv Y, Shiloh Y, Lobrich M, et al. ATM signaling facilitates repair of DNA double-strand breaks associated with heterochromatin. Mol Cell 2008; 31:167 - 177
   PubMed Web of Science ®Google Scholar
• Li X, Lin HH, Chen H, Xu X, Shih HM, Ann DK. SUMOylation of the transcriptional co-repressor KAP1 is regulated by the serine and threonine phosphatase PP1. Sci Signal 2010; 3:32
   Google Scholar
• Zeng L, Yap KL, Ivanov AV, Wang X, Mujtaba S, Plotnikova O, et al. Structural insights into human KAP1 PHD finger-bromodomain and its role in gene silencing. Nat Struct Mol Biol 2008; 15:626 - 633
   PubMed Web of Science ®Google Scholar
• Noon AT, Shibata A, Rief N, Lobrich M, Stewart GS, Jeggo PA, et al. 53BP1-dependent robust localized KAP-1 phosphorylation is essential for heterochromatic DNA double-strand break repair. Nat Cell Biol 2010; 12:177 - 184
   PubMed Web of Science ®Google Scholar
• Goodarzi AA, Noon AT, Jeggo PA. The impact of heterochromatin on DSB repair. Biochem Soc Trans 2009; 37:569 - 576
   PubMed Web of Science ®Google Scholar
• Li X, Lee YK, Jeng JC, Yen Y, Schultz DC, Shih HM, et al. Role for KAP1 serine 824 phosphorylation and sumoylation/desumoylation switch in regulating KAP1-mediated transcriptional repression. J Biol Chem 2007; 282:36177 - 36189
   PubMed Web of Science ®Google Scholar
• Ayoub N, Jeyasekharan AD, Bernal JA, Venkitaraman AR. HP1-beta mobilization promotes chromatin changes that initiate the DNA damage response. Nature 2008; 453:682 - 686
   PubMed Web of Science ®Google Scholar
• Luijsterburg MS, Dinant C, Lans H, Stap J, Wiernasz E, Lagerwerf S, et al. Heterochromatin protein 1 is recruited to various types of DNA damage. J Cell Biol 2009; 185:577 - 586
   PubMed Web of Science ®Google Scholar
• Sun Y, Jiang X, Xu Y, Ayrapetov MK, Moreau LA, Whetstine JR, et al. Histone H3 methylation links DNA damage detection to activation of the tumour suppressor Tip60. Nat Cell Biol 2009; 11:1376 - 1382
   PubMed Web of Science ®Google Scholar
• Murga M, Jaco I, Fan Y, Soria R, Martinez-Pastor B, Cuadrado M, et al. Global chromatin compaction limits the strength of the DNA damage response. J Cell Biol 2007; 178:1101 - 1108
   PubMed Web of Science ®Google Scholar
• Kruhlak MJ, Celeste A, Dellaire G, Fernandez-Capetillo O, Muller WG, McNally JG, et al. Changes in chromatin structure and mobility in living cells at sites of DNA double-strand breaks. J Cell Biol 2006; 172:823 - 834
   PubMed Web of Science ®Google Scholar
• Toth K, Brun N, Langowski J. Chromatin compaction at the mononucleosome level. Biochemistry 2006; 45:1591 - 1598
   PubMed Web of Science ®Google Scholar
• Ferreira H, Somers J, Webster R, Flaus A, Owen-Hughes T. Histone tails and the H3 alphaN helix regulate nucleosome mobility and stability. Mol Cell Biol 2007; 27:4037 - 4048
   PubMed Web of Science ®Google Scholar
• Wang X, Hayes JJ. Acetylation mimics within individual core histone tail domains indicate distinct roles in regulating the stability of higher-order chromatin structure. Mol Cell Biol 2008; 28:227 - 236
   PubMed Web of Science ®Google Scholar
• Choi JK, Howe LJ. Histone acetylation: truth of consequences?. Biochem Cell Biol 2009; 87:139 - 150
   PubMed Web of Science ®Google Scholar
• Murr R, Loizou JI, Yang YG, Cuenin C, Li H, Wang ZQ, et al. Histone acetylation by Trrap-Tip60 modulates loading of repair proteins and repair of DNA double-strand breaks. Nat Cell Biol 2006; 8:91 - 99
   PubMed Web of Science ®Google Scholar
• Downs JA, Allard S, Jobin-Robitaille O, Javaheri A, Auger A, Bouchard N, et al. Binding of Chromatin-Modifying Activities to Phosphorylated Histone H2A at DNA Damage Sites. Mol Cell 2004; 16:979 - 990
   PubMed Web of Science ®Google Scholar
• Bird AW, Yu DY, Pray-Grant MG, Qiu Q, Harmon KE, Megee PC, et al. Acetylation of histone H4 by Esa1 is required for DNA double-strand break repair. Nature 2002; 419:411 - 415
   PubMed Web of Science ®Google Scholar
• Jha S, Shibata E, Dutta A. Human Rvb1/Tip49 is required for the histone acetyltransferase activity of Tip60/NuA4 and for the downregulation of phosphorylation on H2AX after DNA damage. Mol Cell Biol 2008; 28:2690 - 2700
   PubMed Web of Science ®Google Scholar
• Kusch T, Florens L, Macdonald WH, Swanson SK, Glaser RL, Yates JR 3rd, et al. Acetylation by Tip60 is required for selective histone variant exchange at DNA lesions. Science 2004; 306:2084 - 2087
   PubMed Web of Science ®Google Scholar
• Jiang X, Xu Y, Price BD. Acetylation of H2AX on lysine 36 plays a key role in the DNA double-strand break repair pathway. FEBS Lett 2010; 584:2926 - 2930
   PubMed Web of Science ®Google Scholar
• Sun Y, Jiang X, Chen S, Fernandes N, Price BD. A role for the Tip60 histone acetyltransferase in the acetylation and activation of ATM. Proc Natl Acad Sci USA 2005; 102:13182 - 13187
   PubMed Web of Science ®Google Scholar
• Sun Y, Xu Y, Roy K, Price BD. DNA damage-induced acetylation of lysine 3016 of ATM activates ATM kinase activity. Mol Cell Biol 2007; 27:8502 - 8509
   PubMed Web of Science ®Google Scholar
• Sun Y, Jiang X, Price BD. Tip60: Connecting chromatin to DNA damage signaling. Cell Cycle 2010; 9
   Google Scholar
• Birger Y, West KL, Postnikov YV, Lim JH, Furusawa T, Wagner JP, et al. Chromosomal protein HMGN1 enhances the rate of DNA repair in chromatin. EMBO J 2003; 22:1665 - 1675
   PubMed Web of Science ®Google Scholar
• Auger A, Galarneau L, Altaf M, Nourani A, Doyon Y, Utley RT, et al. Eaf1 is the platform for NuA4 molecular assembly that evolutionarily links chromatin acetylation to ATP-dependent exchange of histone H2A variants. Mol Cell Biol 2008; 28:2257 - 2270
   PubMed Web of Science ®Google Scholar
• Doyon Y, Cote J. The highly conserved and multifunctional NuA4 HAT complex. Curr Opin Genet Dev 2004; 14:147 - 154
   PubMed Web of Science ®Google Scholar
• Selleck W, Fortin I, Sermwittayawong D, Cote J, Tan S. The Saccharomyces cerevisiae Piccolo NuA4 histone acetyltransferase complex requires the Enhancer of Polycomb A domain and chromodomain to acetylate nucleosomes. Mol Cell Biol 2005; 25:5535 - 5542
   PubMed Web of Science ®Google Scholar
• Fuchs M, Gerber J, Drapkin R, Sif S, Ikura T, Ogryzko V, et al. The p400 complex is an essential E1A transformation target. Cell 2001; 106:297 - 307
   PubMed Web of Science ®Google Scholar
• Chan HM, Narita M, Lowe SW, Livingston DM. The p400 E1A-associated protein is a novel component of the p53→p21 senescence pathway. Genes Dev 2005; 19:196 - 201
   PubMed Web of Science ®Google Scholar
• Gevry N, Chan HM, Laflamme L, Livingston DM, Gaudreau L. p21 transcription is regulated by differential localization of histone H2A.Z. Genes Dev 2007; 21:1869 - 1881
   PubMed Web of Science ®Google Scholar
• Kusch T, Florens L, Macdonald WH, Swanson SK, Glaser RL, Yates JR 3rd, et al. Acetylation by Tip60 is required for selective histone variant exchange at DNA lesions. Science 2004; 306:2084 - 2087
   PubMed Web of Science ®Google Scholar
• Xu Y, Sun Y, Jiang X, Ayrapetov MK, Moskwa P, Yang S, et al. The p400 ATPase regulates nucleosome stability and chromatin ubiquitination during DNA repair. J Cell Biol 2010; 191:31 - 43
   PubMed Web of Science ®Google Scholar
• Mattera L, Escaffit F, Pillaire MJ, Selves J, Tyteca S, Hoffmann JS, et al. The p400/Tip60 ratio is critical for colorectal cancer cell proliferation through DNA damage response pathways. Oncogene 2009; 28:1506 - 1517
   PubMed Web of Science ®Google Scholar
• Brower-Toland B, Wacker DA, Fulbright RM, Lis JT, Kraus WL, Wang MD. Specific contributions of histone tails and their acetylation to the mechanical stability of nucleosomes. J Mol Biol 2005; 346:135 - 146
   PubMed Web of Science ®Google Scholar
• Altaf M, Auger A, Covic M, Cote J. Connection between histone H2A variants and chromatin remodeling complexes. Biochem Cell Biol 2009; 87:35 - 50
   PubMed Web of Science ®Google Scholar
• von Holt C, Brandt WF, Greyling HJ, Lindsey GG, Retief JD, Rodrigues JD, et al. Isolation and characterization of histones. Methods Enzymol 1989; 170:431 - 523
   PubMed Web of Science ®Google Scholar
• Ye J, Ai X, Eugeni EE, Zhang L, Carpenter LR, Jelinek MA, et al. Histone H4 lysine 91 acetylation a core domain modification associated with chromatin assembly. Mol Cell 2005; 18:123 - 130
   PubMed Web of Science ®Google Scholar
• Luger K, Mader AW, Richmond RK, Sargent DF, Richmond TJ. Crystal structure of the nucleosome core particle at 2.8 A resolution. Nature 1997; 389:251 - 260
   PubMed Web of Science ®Google Scholar
• Chodaparambil JV, Barbera AJ, Lu X, Kaye KM, Hansen JC, Luger K. A charged and contoured surface on the nucleosome regulates chromatin compaction. Nat Struct Mol Biol 2007; 14:1105 - 1107
   PubMed Web of Science ®Google Scholar
• Shogren-Knaak M, Ishii H, Sun JM, Pazin MJ, Davie JR, Peterson CL. Histone H4-K16 acetylation controls chromatin structure and protein interactions. Science 2006; 311:844 - 847
   PubMed Web of Science ®Google Scholar
• Robinson PJ, An W, Routh A, Martino F, Chapman L, Roeder RG, et al. 30 nm chromatin fibre decompaction requires both H4-K16 acetylation and linker histone eviction. J Mol Biol 2008; 381:816 - 825
   PubMed Web of Science ®Google Scholar
• Doyon Y, Selleck W, Lane WS, Tan S, Cote J. Structural and functional conservation of the NuA4 histone acetyltransferase complex from yeast to humans. Mol Cell Biol 2004; 24:1884 - 1896
   PubMed Web of Science ®Google Scholar
• Mailand N, Bekker-Jensen S, Faustrup H, Melander F, Bartek J, Lukas C, et al. RNF8 ubiquitylates histones at DNA double-strand breaks and promotes assembly of repair proteins. Cell 2007; 131:887 - 900
   PubMed Web of Science ®Google Scholar
• Huen MS, Grant R, Manke I, Minn K, Yu X, Yaffe MB, et al. RNF8 transduces the DNA-damage signal via histone ubiquitylation and checkpoint protein assembly. Cell 2007; 131:901 - 914
   PubMed Web of Science ®Google Scholar
• Stewart GS, Panier S, Townsend K, Al-Hakim AK, Kolas NK, Miller ES, et al. The RIDDLE syndrome protein mediates a ubiquitin-dependent signaling cascade at sites of DNA damage. Cell 2009; 136:420 - 434
   PubMed Web of Science ®Google Scholar
• Doil C, Mailand N, Bekker-Jensen S, Menard P, Larsen DH, Pepperkok R, et al. RNF168 binds and amplifies ubiquitin conjugates on damaged chromosomes to allow accumulation of repair proteins. Cell 2009; 136:435 - 446
   PubMed Web of Science ®Google Scholar
• Kim H, Chen J, Yu X. Ubiquitin-binding protein RAP80 mediates BRCA1-dependent DNA damage response. Science 2007; 316:1202 - 1205
   PubMed Web of Science ®Google Scholar
• Sobhian B, Shao G, Lilli DR, Culhane AC, Moreau LA, Xia B, et al. RAP80 targets BRCA1 to specific ubiquitin structures at DNA damage sites. Science 2007; 316:1198 - 1202
   PubMed Web of Science ®Google Scholar
• Wang B, Elledge SJ. Ubc13/Rnf8 ubiquitin ligases control foci formation of the Rap80/Abraxas/Brca1/Brcc36 complex in response to DNA damage. Proc Natl Acad Sci USA 2007; 104:20759 - 20763
   PubMed Web of Science ®Google Scholar
• Urnov FD, Miller JC, Lee YL, Beausejour CM, Rock JM, Augustus S, et al. Highly efficient endogenous human gene correction using designed zinc-finger nucleases. Nature 2005; 435:646 - 651
   PubMed Web of Science ®Google Scholar
• Hockemeyer D, Soldner F, Beard C, Gao Q, Mitalipova M, Dekelver RC, et al. Efficient targeting of expressed and silent genes in human ESCs and iPSCs using zinc-finger nucleases. Nat Biotechnol 2009; 9:851 - 857
   Web of Science ®Google Scholar
• Ikura T, Tashiro S, Kakino A, Shima H, Jacob N, Amunugama R, et al. DNA damage-dependent acetylation and ubiquitination of H2AX enhances chromatin dynamics. Mol Cell Biol 2007; 27:7028 - 7040
   PubMed Web of Science ®Google Scholar
• Sanders SL, Portoso M, Mata J, Bahler J, Allshire RC, Kouzarides T. Methylation of histone H4 lysine 20 controls recruitment of Crb2 to sites of DNA damage. Cell 2004; 119:603 - 614
   PubMed Web of Science ®Google Scholar
• Botuyan MV, Lee J, Ward IM, Kim JE, Thompson JR, Chen J, et al. Structural basis for the methylation state-specific recognition of histone H4-K20 by 53BP1 and Crb2 in DNA repair. Cell 2006; 127:1361 - 1373
   PubMed Web of Science ®Google Scholar
• Huyen Y, Zgheib O, Ditullio RA Jr, Gorgoulis VG, Zacharatos P, Petty TJ, et al. Methylated lysine 79 of histone H3 targets 53BP1 to DNA double-strand breaks. Nature 2004; 432:406 - 411
   PubMed Web of Science ®Google Scholar
• Galanty Y, Belotserkovskaya R, Coates J, Polo S, Miller KM, Jackson SP. Mammalian SUMO E3-ligases PIAS1 and PIAS4 promote responses to DNA double-strand breaks. Nature 2009; 462:935 - 939
   PubMed Web of Science ®Google Scholar
• Morris JR, Boutell C, Keppler M, Densham R, Weekes D, Alamshah A, et al. The SUMO modification pathway is involved in the BRCA1 response to genotoxic stress. Nature 2009; 462:886 - 890
   PubMed Web of Science ®Google Scholar
• Chapman JR, Jackson SP. Phospho-dependent interactions between NBS1 and MDC1 mediate chromatin retention of the MRN complex at sites of DNA damage. EMBO Rep 2008; 9:795 - 801
   PubMed Web of Science ®Google Scholar
• Tworkowski KA, Chakraborty AA, Samuelson AV, Seger YR, Narita M, Hannon GJ, et al. Adenovirus E1A targets p400 to induce the cellular oncoprotein Myc. Proc Natl Acad Sci USA 2008; 105:6103 - 6108
   PubMed Web of Science ®Google Scholar
• Gorrini C, Squatrito M, Luise C, Syed N, Perna D, Wark L, et al. Tip60 is a haplo-insufficient tumour suppressor required for an oncogene-induced DNA damage response. Nature 2007; 448:1063 - 1067
   PubMed Web of Science ®Google Scholar
• Sakuraba K, Yasuda T, Sakata M, Kitamura YH, Shirahata A, Goto T, et al. Downregulation of Tip60 gene as a potential marker for the malignancy of colorectal cancer. Anticancer Res 2009; 29:3953 - 3955
   PubMed Web of Science ®Google Scholar
• Iacovoni JS, Caron P, Lassadi I, Nicolas E, Massip L, Trouche D, et al. High-resolution profiling of gammaH2AX around DNA double strand breaks in the mammalian genome. EMBO J 2010; 29:1446 - 1457
   PubMed Web of Science ®Google Scholar
• Savic V, Yin B, Maas NL, Bredemeyer AL, Carpenter AC, Helmink BA, et al. Formation of dynamic gamma-H2AX domains along broken DNA strands is distinctly regulated by ATM and MDC1 and dependent upon H2AX densities in chromatin. Mol Cell 2009; 34:298 - 310
   PubMed Web of Science ®Google Scholar
• Kim JA, Kruhlak M, Dotiwala F, Nussenzweig A, Haber JE. Heterochromatin is refractory to gamma-H2AX modification in yeast and mammals. J Cell Biol 2007; 178:209 - 218
   PubMed Web of Science ®Google Scholar
• Cowell IG, Sunter NJ, Singh PB, Austin CA, Durkacz BW, Tilby MJ. gammaH2AX foci form preferentially in euchromatin after ionising-radiation. PLoS One 2007; 2:1057
   PubMed Web of Science ®Google Scholar