Chromatin modifiers in transcription and DNA repair

Cellular and Molecular Life Sciences

Volumn 61, Issue 17, 2004, Pages 2154-2162

  Verger, A ^a   Crossley, M ^a  

^a UNIVERSITY OF SYDNEY   (Australia)

Author keywords

Chromatin; DNA damage; Repair; Transcription

Indexed keywords

ADENOSINE TRIPHOSPHATE; DNA; ENZYME; HISTONE;

CHROMATIN STRUCTURE; DNA PACKAGING; DNA RECOMBINATION; DNA REPAIR; DNA REPLICATION; DNA TRANSCRIPTION; EUKARYOTE; EXCISION REPAIR; GENETIC RECOMBINATION; IONIZING RADIATION; MISMATCH REPAIR; NONHUMAN; NUCLEOSOME; PROTEIN MODIFICATION; PROTEIN PROCESSING; REVIEW; X RAY;

ANIMALS; CHROMATIN; DNA REPAIR; HUMANS; TRANSCRIPTION, GENETIC;

EUKARYOTA;

EID: 4644255692     PISSN: 1420682X     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00018-004-4176-y     Document Type: Review

References (82)

1. Friedberg E. C. (2003) DNA damage and repair. Nature 421: 436-440
2. Hoeijmakers J. H. (2001) Genome maintenance mechanisms for preventing cancer. Nature 411: 366-374
3. Khanna K. K. and Jackson S. P. (2001) DNA double-strand breaks: signaling, repair and the cancer connection. Nat. Genet. 27: 247-254
4. Christmann M., Tomicic M. T., Roos W. P. and Kaina B. (2003) Mechanisms of human DNA repair: an update. Toxicology 193: 3-34
5. Friedberg E. C. (2001) How nucleotide excision repair protects against cancer. Nat. Rev. Cancer 1: 22-33
6. Rouse J. and Jackson S. P. (2002) Interfaces between the detection, signaling and repair of DNA damage. Science 297: 547-551
7. Green C. M. and Almouzni G. (2002) When repair meets chromatin. First in series on chromatin dynamics. EMBO Rep. 3: 28-33
8. Ikura T. and Ogryzko V. V. (2003) Chromatin dynamics and DNA repair. Front. Biosci. 8: s149-155
9. Hasan S. and Hottiger M. O. (2002) Histone acetyl transferases: a role in DNA repair and DNA replication. J. Mol. Med. 80: 463-474
10. Ura K. and Hayes J. J. (2002) Nucleotide excision repair and chromatin remodeling. Eur. J. Biochem. 269: 2288-2293
11. Thoma F. (1999) Light and dark in chromatin repair: repair of UV-induced DNA lesions by photolyase and nucleotide excision repair. EMBO J. 18: 6585-6598
12. Gontijo A. M., Green C. M. and Almouzni G. (2003) Repairing DNA damage in chromatin. Biochimie 85: 1133-1147
13. Meijer M. and Smerdon M. J. (1999) Accessing DNA damage in chromatin: insights from transcription. Bioessays 21: 596-603
14. Horn P. J. and Peterson C. L. (2002) Molecular biology. Chromatin higher order folding-wrapping up transcription. Science 297: 1824-1827
15. Narlikar G. J., Fan H. Y. and Kingston R. E. (2002) Cooperation between complexes that regulate chromatin structure and transcription. Cell 108: 475-487
16. Vaquero A., Loyola A. and Reinberg D. (2003) The constantly changing face of chromatin. Sci. Aging Knowl. Environ. 2003: RE4
17. Becker P. B. and Horz W. (2002) ATP-dependent nucleosome remodeling. Annu. Rev. Biochem. 71: 247-273
18. Holstege F. C., Jennings E. G., Wyrick J. J., Lee T. I., Hengartner C. J., Green M. R. et al. (1998) Dissecting the regulatory circuitry of a eukaryotic genome. Cell 95: 717-728
19. Luger K., Mader A. W., Richmond R. K., Sargent D. F. and Richmond T. J. (1997) Crystal structure of the nucleosome core particle at 2.8 A resolution. Nature 389: 251-260
20. Richmond T. J., Finch J. T., Rushton B., Rhodes D. and Klug A. (1984) Structure of the nucleosome core particle at 7 A resolution. Nature 311: 532-537
21. Strahl B. D. and Allis C. D. (2000) The language of covalent histone modifications. Nature 403: 41-45
22. Jenuwein T. and Allis C. D. (2001) Translating the histone code. Science 293: 1074-1080
23. Tora L. (2002) A unified nomenclature for TATA box binding protein (TBP)-associated factors (TAFs) involved in RNA polymerase II transcription. Genes Dev. 16: 673-675
24. Zeng L. and Zhou M. M. (2002) Bromodomain: an acetyl-lysine binding domain. FEBS Lett. 513: 124-128
25. Taunton J., Hassig C. A. and Schreiber S. L. (1996) A mammalian histone deacetylase related to the yeast transcriptional regulator Rpd3p. Science 272: 408-411
26. Rice J. C. and Allis C. D. (2001) Histone methylation versus histone acetylation: new insights into epigenetic regulation. Curr. Opin. Cell Biol. 13: 263-273
27. Ahmad K. and Henikoff S. (2002) Epigenetic consequences of nucleosome dynamics. Cell 111: 281-284
28. Ahmad K. and Henikoff S. (2002) The histone variant H3.3 marks active chromatin by replication-independent nucleosome assembly. Mol. Cell. 9: 1191-2000
29. Wilkins R. J. and Hart R. W. (1974) Preferential DNA repair in human cells. Nature 247: 35-36
30. Jensen K. A. and Smerdon M. J. (1990) DNA repair within nucleosome cores of UV-irradiated human cells. Biochemistry 29: 4773-4782
31. Smerdon M. J. and Thoma F. (1990) Site-specific DNA repair at the nucleosome level in a yeast minichromosome. Cell 61: 675-684
32. Tanaka S., Livingstone-Zatchej M. and Thoma F. (1996) Chromatin structure of the yeast URA3 gene at high resolution provides insight into structure and positioning of nucleosomes in the chromosomal context. J. Mol. Biol. 257: 919-934
33. Wang Z. G., Wu X. H. and Friedberg E. C. (1991) Nucleotide excision repair of DNA by human cell extracts is suppressed in reconstituted nucleosomes. J. Biol. Chem. 266: 22472-22478
34. Sugasawa K., Masutani C. and Hanaoka F. (1993) Cell-free repair of UV-damaged simian virus 40 chromosomes in human cell extracts. I. Development of a cell-free system detecting excision repair of UV-irradiated SV40 chromosomes. J. Biol. Chem. 268: 9098-9104
35. Schieferstein U. and Thoma F. (1998) Site-specific repair of cyclobutane pyrimidine dimers in a positioned nucleosome by photolyase and T4 endonuclease V in vitro. EMBO J. 17: 306-316
36. Liu X. and Smerdon M. J. (2000) Nucleotide excision repair of the 5 S ribosomal RNA gene assembled into a nucleosome. J. Biol. Chem. 275: 23729-23735
37. Hara R., Mo J. and Sancar A. (2000) DNA damage in the nucleosome core is refractory to repair by human excision nuclease. Mol. Cell. Biol. 20: 9173-9181
38. Ura K., Araki M., Saeki H., Masutani C., Ito T., Iwai S. et al. (2001) ATP-dependent chromatin remodeling facilitates nucleotide excision repair of UV-induced DNA lesions in synthetic dinucleosomes. EMBO J. 20: 2004-2014
39. Kosmoski J. V., Ackerman E. J. and Smerdon M. J. (2001) DNA repair of a single UV photoproduct in a designed nucleosome. Proc. Natl. Acad. Sci. USA 98: 10113-10118
40. Nilsen H., Lindahl T. and Verreault A. (2002) DNA base excision repair of uracil residues in reconstituted nucleosome core particles. EMBO J. 21: 5943-5952
41. Shen X., Mizuguchi G., Hamiche A. and Wu C. (2000) A chromatin remodelling complex involved in transcription and DNA processing. Nature 406: 541-544
42. Jonsson Z. O., Dhar S. K., Narlikar G. J., Auty R., Wagle N., Pellman D. et al. (2001) Rvb1p and Rvb2p are essential components of a chromatin remodeling complex that regulates transcription of over 5% of yeast genes. J. Biol. Chem. 276: 16279-16288
43. Huang J. C. and Sancar A. (1994) Determination of minimum substrate size for human excinuclease. J. Biol. Chem. 269: 19034-19040
44. Hara R. and Sancar A. (2002) The SWI/SNF chromatin-remodeling factor stimulates repair by human excision nuclease in the mononucleosome core particle. Mol. Cell. Biol. 22: 6779-6787
45. Hara R. and Sancar A. (2003) Effect of damage type on stimulation of human excision nuclease by SWI/SNF chromatin remodeling factor. Mol. Cell. Biol. 23: 4121-4125
46. Gaillard H., Fitzgerald D. J., Smith C. L., Peterson C. L., Richmond T. J. and Thoma F. (2003) Chromatin remodeling activities act on UV-damaged nucleosomes and modulate DNA damage accessibility to photolyase. J. Biol. Chem. 278: 17655-17663
47. Eisen J. A., Sweder K. S. and Hanawalt P. C. (1995) Evolution of the SNF2 family of proteins: subfamilies with distinct sequences and functions. Nucleic Acids Res. 23: 2715-2723
48. Citterio E., Van Den Boom V., Schnitzler G., Kanaar R., Bonte E., Kingston R. E. et al. (2000) ATP-dependent chromatin remodeling by the Cockayne syndrome B DNA repair-transcription-coupling factor. Mol. Cell. Biol. 20: 7643-7653
49. Guzder S. N., Sung P., Prakash L. and Prakash S. (1998) Affinity of yeast nucleotide excision repair factor 2, consisting of the Rad4 and Rad23 proteins, for ultraviolet damaged DNA. J. Biol. Chem. 273: 31541-31546
50. Guzder S. N., Sung P., Prakash L. and Prakash S. (1998) The DNA-dependent ATPase activity of yeast nucleotide excision repair factor 4 and its role in DNA damage recognition. J. Biol. Chem. 273: 6292-6296
51. Alexeev A., Mazin A. and Kowalczykowski S. C. (2003) Rad54 protein possesses chromatin-remodeling activity stimulated by the Rad51-ssDNA nucleoprotein filament. Nat. Struct. Biol. 10: 182-186
52. Alexiadis V. and Kadonaga J. T. (2002) Strand pairing by Rad54 and Rad51 is enhanced by chromatin. Genes Dev. 16: 2767-2771
53. Ridgway P. and Almouzni G. (2000) CAF-1 and the inheritance of chromatin states: at the crossroads of DNA replication and repair. J. Cell Sci. 113(Pt 15): 2647-2658
54. Gaillard P. H., Martini E. M., Kaufman P. D., Stillman B., Moustacchi E. and Almouzni G. (1996) Chromatin assembly coupled to DNA repair: a new role for chromatin assembly factor I. Cell 86: 887-896
55. Green C. M. and Almouzni G. (2003) Local action of the chromatin assembly factor CAF-1 at sites of nucleotide excision repair in vivo. EMBO J. 22: 5163-5174
56. Moggs J. G., Grandi P., Quivy J. P., Jonsson Z. O., Hubscher U., Becker P. B. et al. (2000) A CAF-1-PCNA-mediated chromatin assembly pathway triggered by sensing DNA damage. Mol. Cell. Biol. 20: 1206-1218
57. Rubbi C. P. and Milner J. (2003) P53 is a chromatin accessibility factor for nucleotide excision repair of DNA damage. EMBO J. 22: 975-986
58. Brand M., Moggs J. G., Oulad-Abdelghani M., Lejeune F., Dilworth F. J., Stevenin J. et al. (2001) UV-damaged DNA-binding protein in the TFTC complex links DNA damage recognition to nucleosome acetylation. EMBO J. 20: 3187-3196
59. Qin S. and Parthun M. R. (2002) Histone H3 and the histone acetyltransferase Hat1p contribute to DNA double-strand break repair. Mol. Cell. Biol. 22: 8353-8365
60. Ikura T., Ogryzko V. V., Grigoriev M., Groisman R., Wang J., Horikoshi M. et al. (2000) Involvement of the TIP60 histone acetylase complex in DNA repair and apoptosis. Cell 102: 463-473
61. Bird A. W., Yu D. Y., Pray-Grant M. G., Qiu Q., Harmon K. E., Megee P. C. et al. (2002) Acetylation of histone H4 by Esa1 is required for DNA double-strand break repair. Nature 419: 411-415
62. Datta A., Bagchi S., Nag A., Shiyanov P., Adami G. R., Yoon T. et al. (2001) The p48 subunit of the damaged-DNA binding protein DDB associates with the CBP/p300 family of histone acetyltransferase. Mutat. Res. 486: 89-97
63. Martinez E., Palhan V. B., Tjernberg A., Lymar E. S., Gamper A. M., Kundu T. K. et al. (2001) Human STAGA complex is a chromatin-acetylating transcription coactivator that interacts with pre-mRNA splicing and DNA damage-binding factors in vivo. Mol. Cell. Biol. 21: 6782-6795
64. Tini M., Benecke A., Um S. J., Torchia J., Evans R. M. and Chambon P. (2002) Association of CBP/p300 acetylase and thymine DNA glycosylase links DNA repair and transcription. Mol. Cell. 9: 265-277
65. Hasan S., Hassa P. O., Imhof R. and Hottiger M. O. (2001) Transcription coactivator p300 binds PCNA and may have a role in DNA repair synthesis. Nature 410: 387-391
66. Hasan S., Stucki M., Hassa P. O., Imhof R., Gehrig P., Hunziker P. et al. (2001) Regulation of human flap endonuclease-1 activity by acetylation through the transcriptional coactivator p300. Mol. Cell. 7: 1221-1231
67. Tsukamoto Y., Kato J. and Ikeda H. (1997) Silencing factors participate in DNA repair and recombination in Saccharomyces cerevisiae. Nature 388: 900-903
68. Vaziri H., Dessain S. K., Ng Eaton E., Imai S. I., Frye R. A., Pandita T. K. et al. (2001) hSIR2(SIRT1) functions as an NAD-dependent p53 deacetylase. Cell 107: 149-159
69. Luo J., Nikolaev A. Y., Imai S., Chen D., Su F., Shiloh A. et al. (2001) Negative control of p53 by Sir2alpha promotes cell survival under stress. Cell 107: 137-148
70. Garcia-Salcedo J. A., Gijon P., Nolan D. P., Tebabi P. and Pays E. (2003) A chromosomal SIR2 homologue with both histone NAD-dependent ADP-ribosyltransferase and deacetylase activities is involved in DNA repair in Trypanosoma brucei. EMBO J. 22: 5851-5862
71. Bouchard V. J., Rouleau M. and Poirier G. G. (2003) PARP-1, a determinant of cell survival in response to DNA damage. Exp. Hematol. 31: 446-454
72. Poirier G. G., de Murcia G., Jongstra-Bilen J., Niedergang C. and Mandel P. (1982) Poly(ADP-ribosyl)ation of polynucleosomes causes relaxation of chromatin structure. Proc. Natl. Acad. Sci. USA 79: 3423-3427
73. Tulin A., Stewart D. and Spradling A. C. (2002) The Drosophila heterochromatic gene encoding poly(ADP-ribose) polymerase (PARP) is required to modulate chromatin structure during development. Genes Dev. 16: 2108-2119
74. Bustin M. (2001) Chromatin unfolding and activation by HMGN(*) chromosomal proteins. Trends Biochem. Sci. 26: 431-437
75. Birger Y., West K. L., Postnikov Y. V., Lim J. H., Furusawa T., Wagner J. P. et al. (2003) Chromosomal protein HMGN1 enhances the rate of DNA repair in chromatin. EMBO J. 22: 1665-1675
76. Svejstrup J. Q. (2002) Mechanisms of transcription-coupled DNA repair. Nat. Rev. Mol. Cell. Biol. 3: 21-29
77. Frit P., Kwon K., Coin F., Auriol J., Dubaele S., Salles B. et al. (2002) Transcriptional activators stimulate DNA repair. Mol. Cell. 10: 1391-1401
78. Rochette-Egly C., Adam S., Rossignol M., Egly J. M. and Chambon P. (1997) Stimulation of RAR alpha activation function AF-1 through binding to the general transcription factor TFIIH and phosphorylation by CDK7. Cell 90: 97-107
79. Redon C., Pilch D., Rogakou E., Sedelnikova O., Newrock K. and Bonner W. (2002) Histone H2A variants H2AX and H2AZ. Curr. Opin. Genet. Dev. 12: 162-169
80. Modesti M. and Kanaar R. (2001) DNA repair: spot(light)s on chromatin. Curr. Biol. 11: R229-332
81. Celeste A., Fernandez-Capetillo O., Kruhlak M. J., Pilch D. R., Staudt D. W., Lee A. et al. (2003) Histone H2AX phosphorylation is dispensable for the initial recognition of DNA breaks. Nat. Cell. Biol. 5: 675-679
82. Pothof J., van Haaften G., Thijssen K., Kamath R. S., Fraser A. G., Ahringer J. et al. (2003) Identification of genes that protect the C. elegans genome against mutations by genome-wide RNAi. Frequent germline mutations and somatic repeat instability in DNA mismatch-repair-deficient Caenorhabditis elegans. Genes Dev. 17: 443-448