Overview for the histone codes for DNA repair

Progress in Molecular Biology and Translational Science

Volumn 110, Issue , 2012, Pages 207-227

  Williamson, Elizabeth A ^a   Wray, Justin W ^b   Bansal, Pranshu ^b   Hromas, Robert ^a  

^a UNIVERSITY OF FLORIDA COLLEGE OF MEDICINE   (United States)

^b UNIVERSITY OF NEW MEXICO   (United States)

Author keywords

Acetylation; DNA repair; Histone; Methylation; Phosphorylation; Ubiquitylation

Indexed keywords

EID: 84862985041     PISSN: 18771173     EISSN: None     Source Type: Book Series    
DOI: 10.1016/B978-0-12-387665-2.00008-0     Document Type: Chapter

References (94)

1. B. Evers, T. Helleday, and T.J. Jonkers Targeting homologous recombination repair defects in cancer Trends Pharmacol Sci 31 2010 372 380
2. J.D. Moore, and J.E. Krebs Histone modifications and DNA double-strand break repair Biochem Cell Biol 82 2004 446 452 (Pubitemid 39286959)
3. A. Xie, A. Hartlerode, M. Stucki, S. Odate, N. Puget, and A. Kwok Distinct roles of chromatin-associated proteins MDC1 and 53BP1 in mammalian double-strand break repair Mol Cell 28 2007 1045 1057 (Pubitemid 350297033)
4. J. Yuan, R. Adamski, and J. Chen Focus on histone variant H2AX: to be or not to be FEBS Letts 584 2010 3717 3724
5. K.L. Cann, and G. Dellaire Heterochromatin and the DNA damage response: the need to relax Biochem Cell Biol 89 2011 45 60
6. M. Kalocsay, N.J. Hiller, and S. Jentsch Chromosome-wide Rad51 spreading and SUMO-H2A.Z-dependent chromosome fixation in response to a persistent DNA double-strand break Mol Cell 33 2009 335 343
7. Y. Xu, Y. Sun, X. Jiang, M.K. Ayrapetov, P. Moskwa, and S. Yang The p400 ATPase regulates nucleosome stability and chromatin ubiquitination during DNA repair J Cell Biol 191 2010 31 43
8. Y. Sun, X. Jiang, and B.D. Price Tip60: connecting chromatin to DNA damage signaling Cell Cycle 9 2010 930 936
9. M. Giannattasio, F. Lazzaro, P. Plevani, and M. Muzi-Falconi The DNA damage checkpoint response requires histone H2B ubiquitination by Rad6-Bre1 and H3 methylation by Dot1 J Biol Chem 280 2005 9879 9886 (Pubitemid 40395835)
10. R. Wysocki, A. Javaheri, S. Allard, F. Sha, J. Cote, and S.J. Kron Role of Dot1-dependent histone H3 methylation in G1 and S phase DNA damage checkpoint functions of Rad9 Mol Cell Biol 25 2005 8430 8443 (Pubitemid 41369165)
11. D. Huertas, R. Sendra, and P. Munoz Chromatin dynamics coupled to DNA repair Epigenetics 4 2009 31 42
12. B.A. Tamburini, and J.K. Tyler Localized histone acetylation and deacetylation triggered by the homologous recombination pathway of double-strand DNA repair Mol Cell Biol 25 2005 4903 4913 (Pubitemid 40781092)
13. R. Murr, J.I. Loizou, Y.G. Yang, C. Cuenin, H. Li, and Z.Q. Wang Histone acetylation by Trrap-Tip60 modulates loading of repair proteins and repair of DNA double-strand breaks Nat Cell Biol 8 2006 91 99 (Pubitemid 43064802)
14. S. Qin, and M.R. Parthun Histone H3 and the histone acetyltransferase Hat1p contribute to DNA double-strand break repair Mol Cell Biol 22 2002 8353 8365 (Pubitemid 35304066)
15. H. van Attikum, O. Fritsch, B. Hohn, and S.M. Gasser Recruitment of the INO80 complex by H2A phosphorylation links ATP-dependent chromatin remodeling with DNA double-strand break repair Cell 119 2004 777 788 (Pubitemid 40017685)
16. T. Tsukuda, A.B. Fleming, J.A. Nickoloff, and M.A. Osley Chromatin remodelling at a DNA double-strand break site in Saccharomyces cerevisiae Nature 438 2005 379 383 (Pubitemid 41643956)
17. P. Cheung, K.G. Tanner, W.L. Cheung, P. Sassone-Corsi, J.M. Denu, and C.D. Allis Synergistic coupling of histone H3 phosphorylation and acetylation in response to epidermal growth factor stimulation Mol Cell 5 2000 905 915
18. N.A. Barlev, V. Poltoratsky, T. Owen-Hughes, C. Ying, L. Liu, and J.L. Workman Repression of GCN5 histone acetyltransferase activity via bromodomain-mediated binding and phosphorylation by the Ku-DNA-dependent protein kinase complex Mol Cell Biol 18 1998 1349 1358 (Pubitemid 28100899)
19. H. Oishi, H. Kitagawa, O. Wada, S. Takezawa, L. Tora, and M. Kouzu-Fujita An hGCN5/TRRAP histone acetyltransferase complex co-activates BRCA1 transactivation function through histone modification J Biol Chem 281 2006 20 26 (Pubitemid 43671158)
20. N. Mailand, S. Bekker-Jensen, H. Faustrup, F. Melander, J. Bartek, and C. Lukas RNF8 ubiquitylates histones at DNA double-strand breaks and promotes assembly of repair proteins Cell 131 2007 887 900 (Pubitemid 350138084)
21. J.R. Morris, and E. Solomon BRCA1: BARD1 induces the formation of conjugated ubiquitin structures, dependent on K6 of ubiquitin, in cells during DNA replication and repair Hum Mol Genet 13 2004 807 817 (Pubitemid 38515210)
22. E.J. Bennett, and J.W. Harper DNA damage: ubiquitin marks the spot Nat Struct Mol Biol 15 2008 20 22
23. K. Hofmann Ubiquitin-binding domains and their role in the DNA damage response DNA Repair 8 2009 544 556
24. A.J. Morrison, and X. Shen Chromatin remodelling beyond transcription: the INO80 and SWR1 complexes Nat Rev Mol Cell Biol 10 2009 373 384
25. J.A. Downs, S. Allard, O. Jobin-Robitaille, A. Javaheri, A. Auger, and N. Bouchard Binding of chromatin-modifying activities to phosphorylated histone H2A at DNA damage sites Mol Cell 16 2004 979 990 (Pubitemid 40018407)
26. H. van Attikum, O. Fritsch, and S.M. Gasser Distinct roles for SWR1 and INO80 chromatin remodeling complexes at chromosomal double-strand breaks EMBO J 26 2007 4113 4125 (Pubitemid 47462094)
27. T. Kusch, L. Florens, W.H. Macdonald, S.K. Swanson, R.L. Glaser, and J.R. Yates 3rd Acetylation by Tip60 is required for selective histone variant exchange at DNA lesions Science 306 2004 2084 2087 (Pubitemid 40007658)
28. T. Tsukuda, Y.C. Lo, S. Krishna, R. Sterk, M.A. Osley, and J.A. Nickoloff INO80-dependent chromatin remodeling regulates early and late stages of mitotic homologous recombination DNA Repair 8 2009 360 369
29. M. Sinha, S. Watanabe, A. Johnson, D. Moazed, and C.L. Peterson Recombinational repair within heterochromatin requires ATP-dependent chromatin remodeling Cell 138 2009 1109 1121
30. R. Shroff, A. Arbel-Eden, D. Pilch, G. Ira, W.M. Bonner, and J.H. Petrini Distribution and dynamics of chromatin modification induced by a defined DNA double-strand break Curr Biol 14 2004 1703 1711 (Pubitemid 39301159)
31. M. Sinha, and C.L. Peterson Chromatin dynamics during repair of chromosomal DNA double-strand breaks Epigenomics 1 2009 371 385
32. M. Sinha, and C.L. Peterson A Rad51 presynaptic filament is sufficient to capture nucleosomal homology during recombinational repair of a DNA double-strand break Mol Cell 30 2008 803 810 (Pubitemid 351815124)
33. D. Chowdhury, M.C. Keogh, H. Ishii, C.L. Peterson, S. Buratowski, and J. Lieberman gamma-H2AX dephosphorylation by protein phosphatase 2A facilitates DNA double-strand break repair Mol Cell 20 2005 801 809 (Pubitemid 41740701)
34. A. Nabatiyan, D. Szuts, and T. Krude Induction of CAF-1 expression in response to DNA strand breaks in quiescent human cells Mol Cell Biol 26 2006 1839 1849
35. C.C. Chen, J.J. Carson, J. Feser, B. Tamburini, S. Zabaronick, and J. Linger Acetylated lysine 56 on histone H3 drives chromatin assembly after repair and signals for the completion of repair Cell 134 2008 231 243 (Pubitemid 352010334)
36. S. Fnu, E.A. Williamson, L.P. De Haro, M. Brenneman, J. Wray, and M. Shaheen Methylation of histone H3 lysine 36 enhances DNA repair by nonhomologous end-joining Proc Natl Acad Sci U S A 108 2011 540 545
37. S.H. Lee, M. Oshige, S.T. Durant, K.K. Rasila, E.A. Williamson, and H. Ramsey The SET domain protein Metnase mediates foreign DNA integration and links integration to nonhomologous end-joining repair Proc Natl Acad Sci U S A 102 2005 18075 18080 (Pubitemid 41798504)
38. A.E. Escargueil, D.G. Soares, M. Salvador, A.K. Larsen, and J.A. Henriques What histone code for DNA repair? Mutat Res 658 2008 259 270
39. O.A. Sedelnikova, D.R. Pilch, C. Redon, and W.M. Bonner Histone H2AX in DNA damage and repair Cancer Biol Ther 2 2003 233 235
40. M.S. Huen, R. Grant, I. Manke, K. Minn, X. Yu, and M.B. Yaffe RNF8 transduces the DNA damage signal via histone ubiquitylation and checkpoint protein assembly Cell 131 2007 901 914 (Pubitemid 350138083)
41. B. Sobhian, G. Shao, D.R. Lilli, A.C. Culhane, L.A. Moreau, and B. Xie RAP80 target BRCA1 to specific ubiquitin structures at DNA damage sites Science 316 2007 1198 1202 (Pubitemid 46877483)
42. H. Kim, J. Chen, and X. Yu Ubiquitin-binding protein RAP80 mediates BRCA1-dependent DNA damage response Science 316 2007 1202 1205 (Pubitemid 46877484)
43. D. Faucher, and R.J. Wellinger Methylated H3K4, a transcription- associated histone modification, is involved in the DNA damage response PLoS Genet 6 2010 e1001082
44. A.W. Bird, D.Y. Yu, M.G. Pray-Grant, Q. Qiu, K.E. Harmon, and P.C. Megee Acetylation of histone H4 by Esa1 is required for DNA double-strand break repair Nature 419 2002 411 415
45. E.Y. Shim, J.L. Ma, J.H. Oum, Y. Yanez, and S.E. Lee The yeast chromatin remodeler RSC complex facilitates end joining repair of DNA double-strand breaks Mol Cell Biol 25 2005 3934 3944 (Pubitemid 40617645)
46. E.Y. Shim, S.J. Hong, J.H. Oum, Y. Yanez, Y. Zhang, and S.E. Lee RSC mobilizes nucleosomes to improve accessibility of repair machinery to the damaged chromatin Mol Cell Biol 27 2007 1602 1613
47. H. Ogiwara, A. Ui, A. Otsuka, H. Satoh, I. Yokomi, and S. Nakajima Histone acetylation by CBP and p300 at double-strand break sites facilitates SWI/SNF chromatin remodeling and the recruitment of non-homologous end joining factors Oncogene 30 2011 2135 2146
48. A. Jazayeri, A.D. McAinsh, and S.P. Jackson Saccharomyces cerevisiae Sin3p facilitates double-strand break repair Proc Natl Acad Sci U S A 101 2004 1644 1649 (Pubitemid 38234208)
49. W.L. Cheung, F.B. Turner, T. Krishnamoorthy, B. Wolner, S.H. Ahn, and M. Foley Phosphorylation of histone H4 serine 1 during DNA damage requires casein kinase II in S. cerevisiae Curr Biol 15 2005 656 660
50. R.T. Utley, N. Lacoste, O. Jobin-Robitaille, S. Allard, and J. Cote Regulation of NuA4 histone acetyltransferase activity in transcription and DNA repair by phosphorylation of histone H4 Mol Cell Biol 25 2005 8179 8190 (Pubitemid 41263009)
51. Y. Ataian, and J.E. Krebs Five repair pathways in one context: chromatin modification during DNA repair Biochem Cell Biol 84 2006 490 504 (Pubitemid 44703653)
52. E.J. Park, D.W. Chan, J.H. Park, M.A. Oettinger, and J. Kwon DNA-PK is activated by nucleosomes and phosphorylated H2AX within the nucelosomes in an acetylation-dependent manner Nucleic Acids Res 31 2003 6819 6827 (Pubitemid 37508789)
53. A. Li, Y. Yu, S.C. Lee, T. Ishibashi, S.P. Lees-Miller, and J. Ausio Phosphorylation of hisotne H2A.X by DNA-dependent protein kinase is not affected by core histone acetylation but it alters nucleosome stability and histone H1 binding J Biol Chem 285 2010 17778 17788
54. Q. Yan, S. Dutt, R. Xu, K. Graves, P. Juszczynski, and J.P. Manis BBAP monoubiquitylates histone H4 at lysine 91 and selectively modulates the DNA damage response Mol Cell 36 2009 110 120
55. K. Sugasawa, J.M. Ng, C. Masutani, S. Iwai, P.J. van der Spek, and A.P. Eker Xeroderma pigmentosum group C protein complex is the initiator of global genome nucleotide excision repair Mol Cell 2 1998 223 232 (Pubitemid 128373647)
56. A.J. van Gool, E. Citterio, S. Rademakers, R. van Os, W. Vermeulen, and A. Constantinou The Cockayne syndrome B protein, involved in transcription-coupled DNA repair, resides in an RNA polymerase II-containing complex EMBO J 16 1997 5955 5965 (Pubitemid 27427291)
57. S.L. Dresler Stimulation of deoxyribonucleic acid excision repair in human fibroblasts pretreated with sodium butyrate Biochemistry 24 1985 6861 6869 (Pubitemid 16170215)
58. B. Ramanathan, and M.J. Smerdon Enhanced DNA repair synthesis in hyperacetylated nucleosomes J Biol Chem 264 1989 11026 11034 (Pubitemid 19168826)
59. M.J. Smerdon, S.Y. Lan, R.E. Calza, and R. Reeves Sodium butyrate stimulates DNA repair in UV-irradiated normal and xeroderma pigmentosum human fibroblasts J Biol Chem 257 1982 13441 13447 (Pubitemid 13188960)
60. M. Brand, J.G. Moggs, M. Oulad-Abdelghani, F. Lejeune, F.J. Dilworth, and J. Stevenin UV-damaged DNA-binding protein in the TFTC complex links DNA damage recognition to nucleosome acetylation EMBO J 20 2001 3187 3196 (Pubitemid 32612006)
61. M. Brand, K. Yamamoto, A. Staub, and L. Tora Identification of TATA-binding protein-free TAFII-containing complex subunits suggests a role in nucleosome acetylation and signal transduction J Biol Chem 274 1999 18285 18289
62. S.J. Allison, and J. Milner Loss of p53 has site-specific effects on histone H3 modification, including serine 10 phosphorylation important for maintenance of ploidy Cancer Res 63 2003 6674 6679 (Pubitemid 37322946)
63. R. Guo, J. Chen, D.L. Mitchell, and D.G. Johnson GCN5 and E2F1 stimulate nucleotide excision repair by promoting H3K9 acetylation at sites of damage Nucleic Acids Res 2010 2010 1 8
64. S. Chaudhuri, J.J. Wyrick, and M.J. Smerdon Histone H3 Lys70 methylation is required for efficient nucleotide excision repair in a silenced locus of Saccharomyces cerevisiae Nucleic Acids Res 37 2009 1690 1700
65. T.M. Nakamuran, L.L. Du, C. Redon, and P. Russel Histone H2A phosphorylation controls Crb2 recruitment at DNA breaks, maintains checkpoint arrest, and influences DNA repair in fission yeast Mol Cell Biol 24 2004 6215 6230 (Pubitemid 38891124)
66. M. Matsumoto, K. Yaginuma, A. Igarashi, M. Imura, M. Hasegawa, and K. Iwabuchi Perturbed gap-filling synthesis in nucleotide excision repair causes histone H2AX phosphorylation in human quiescent cells J Cell Sci 120 2007 1104 1112 (Pubitemid 46638523)
67. S. Bergink, F.A. Salomons, D. Hoogstraten, T.A. Groothuis, H. de Waard, and J. Wu DNA damage triggers nucleotide excision repair-dependent monoubiquitylation of histone H2A Genes Dev 20 2006 1343 1352 (Pubitemid 43727594)
68. K.K. Bhakat, T.K. Hazra, and S. Mitra Acetylation of the human DNA glycosylase NEIL2 and inhibition of its activity Nucleic Acids Res 32 2004 3033 3039 (Pubitemid 39022994)
69. S. Hasan, M. Stucki, P.O. Hassa, R. Imhof, P. Gehrig, and P. Hunziker Regulation of human flap endonuclease-1 activity by acetylation through the transcriptional coactivator p300 Mol Cell 7 2001 1221 1231 (Pubitemid 32607356)
70. S. Hasan, N. El-Andaloussi, U. Hardeland, P.O. Hassa, C. Burki, and R. Imhof Acetylation regulates the DNA end-trimming activity of DNA polymerase beta Mol Cell 10 2002 1213 1222 (Pubitemid 35453837)
71. G. Henneke, S. Koundrioukoff, and U. Hubscher Phosphorylation of human Fen1 by cyclin-dependent kinase modulates its role in replication fork regulation Oncogene 22 2003 4301 4313 (Pubitemid 36897962)
72. M. Tini, A. Benecke, S.J. Um, J. Torchia, R.M. Evans, and P. Chambon Association of CBP/p300 acetylase and thymine DNA glycosylase links DNA repair and transcription Mol Cell 9 2002 265 277 (Pubitemid 34195553)
73. P. Adamietz, and A. Rudolph ADP-ribosylation of nuclear proteins in vivo. Identification of histone H2B as a major acceptor for mono- and poly(ADP-ribose) in dimethyl sulfate-treated hepatoma AH 7974 cells J Biol Chem 259 1984 6841 6846 (Pubitemid 14078980)
74. A. Kreimeyer, K. Wielckens, P. Adamietz, and H. Hilz DNA repair-associated ADP-ribosylation in vivo. Modification of histone H1 differs from that of the principal acceptor proteins J Biol Chem 259 1984 890 896 (Pubitemid 14192439)
75. K. Wielckens, R. Bredehorst, P. Adamietz, and H. Hilz Mono ADP-ribosylation and poly ADP-ribosylation of proteins in normal and malignant tissues Adv Enzyme Regul 20 1982 23 37
76. L.O. Burzio, P.T. Riquelme, and S.S. Koide ADP ribosylation of rat liver nucleosomal core histones J Biol Chem 254 1979 3029 3037
77. N. Ogata, K. Ueda, and O. Hayaishi ADP-ribosylation of histone H2B. Identification of glutamic acid residue 2 as the modification site J Biol Chem 255 1980 7610 7615
78. N. Ogata, K. Ueda, H. Kagamiyama, and O. Hayaishi ADP-ribosylation of histone H1. Identification of glutamic acid residues 2, 14, and the COOH-terminal lysine residue as modification sites J Biol Chem 255 1980 7616 7620
79. T. Ushiroyama, Y. Tanigawa, M. Tsuchiya, R. Matsuura, M. Ueki, and O. Sugimoto Amino acid sequence of histone H1 at the ADP-ribose-accepting site and ADP-ribose X histone-H1 adduct as an inhibitor of cyclic-AMP-dependent phosphorylation Eur J Biochem 151 1985 173 177 (Pubitemid 15226656)
80. G. Golderer, and P. Grobner ADP-ribosylation of core histones and their acetylated subspecies Biochem J 277 1991 607 610
81. L. Bohm, F.A. Schneeweiss, R.N. Sharan, and L.E. Feinendegen Influence of histone acetylation on the modification of cytoplasmic and nuclear proteins by ADP-ribosylation in response to free radicals Biochim Biophys Acta 1334 1997 149 154 (Pubitemid 27117516)
82. J.A. Garcia-Salcedo, P. Gijon, D.P. Nolan, P. Tebabi, and E. Pays A chromosomal SIR2 homologue with both histone NADdependent ADP-ribosyltransferase and deacetylase activities is involved in DNA repair in Trypanosoma brucei EMBO J 22 2003 5851 5862 (Pubitemid 37408823)
83. G. Marra, and P. Schar Recognition of DNA alterations by the mismatch repair system Biochem J 338 1999 1 13 (Pubitemid 29097278)
84. P. Hsieh Molecular mechanisms of DNA mismatch repair Mutat Res 486 2001 71 87 (Pubitemid 32568409)
85. T.A. Kunkel, and D.A. Erie DNA mismatch repair Annu Rev Biochem 74 2005 681 710 (Pubitemid 40995521)
86. J. Jirincy The multifaceted mismatch-repair system Nat Rev Mol Cell Biol 7 2006 335 346
87. A.S. Mastrocola, and C.D. Heinen Nuclear reorganization of DNA mismatch repair proteins in response to DNA damage DNA Repair 9 2010 120 133
88. H. Flores-Rozas, D. Clark, and R.D. Kolodner Proliferating cell nuclear antigen and Msh2p-Msh6p interact to form an active misrepair recognition complex Nat Genet 26 2000 375 378
89. H.E. Kleczkowska, G. Marra, T. Lettieri, and J. Jirincy hMSH3 and hMSH6 interact with PCNA and colocalize with it to replication foci Genes Dev 15 2001 724 736 (Pubitemid 32244901)
90. A. Groth, W. Rocha, A. Verreault, and G. Almouzni Chromatin challenges during DNA replication and repair Cell 128 2007 721 733 (Pubitemid 46273574)
91. Y. Zhang, F. Yuan, S.R. Presnell, K. Tian, Y. Gao, and A.E. Tomkinson Reconstitution of 5′-directed human mismatched repair in a purified system Cell 122 2005 693 705 (Pubitemid 41242635)
92. J.D. Hawk, L. Stefanovic, J.C. Boyer, T.D. Petes, and R.A. Farber Variation in efficiency of DNA mismatch repair at different sites in the yeast genome Proc Natl Acad Sci U S A 102 2005 8639 8643 (Pubitemid 40862788)
93. F.J. Rodriguez-Jimenez, V. Moreno-Manzano, R. Lucas-Dominguez, and J.M. Sanchez-Puelles Hypoxia causes downregulation of mismatch repair system and genomic instability in stem cells Stem Cells 26 2008 2052 2062
94. S. Javaid, M. Manohar, N. Punja, A. Mooney, J.J. Ottesen, and M.G. Poirer Nucleosome remodeling by hMSH2-hMSH6 Mol Cell 36 2011 1086 1094