Damage site chromatin: Open or closed?

Current Opinion in Cell Biology

Volumn 23, Issue 3, 2011, Pages 277-283

  Ball, Alexander R ^a   Yokomori, Kyoko ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

NICOTINAMIDE ADENINE DINUCLEOTIDE ADENOSINE DIPHOSPHATE RIBOSYLTRANSFERASE; NICOTINAMIDE ADENINE DINUCLEOTIDE ADENOSINE DIPHOSPHATE RIBOSYLTRANSFERASE 1;

CHEMICAL ANALYSIS; CHROMATIN; CHROMATIN IMMUNOPRECIPITATION; CYTOLOGY; DNA DAMAGE; DNA REPAIR; ENZYME ACTIVITY; FLUORESCENCE LOSS IN PHOTOBLEACHING; FLUORESCENCE RECOVERY AFTER PHOTOBLEACHING; FLUORESCENCE RESONANCE ENERGY TRANSFER; FLUOROMETRY; HETEROCHROMATIN; HUMAN; IN VIVO STUDY; NONHUMAN; PRIORITY JOURNAL; PROTEIN PROCESSING; REVIEW; SIGNAL TRANSDUCTION;

ANIMALS; CHROMATIN; CHROMATIN ASSEMBLY AND DISASSEMBLY; DNA DAMAGE; DNA REPAIR; HISTONE CODE; HISTONES; HUMANS; POLY(ADP-RIBOSE) POLYMERASES;

EID: 79957852568     PISSN: 09550674     EISSN: 18790410     Source Type: Journal    
DOI: 10.1016/j.ceb.2011.03.012     Document Type: Review

References (58)

1. Ciccia A., Elledge S.J. The DNA damage response: making it safe to play with knives. Mol Cell 2010, 40:179-204.
2. Kim J.-S., Heale J.T., Zeng W., Kong X., Ball J.A.R., Yokomori K. In situ analysis of DNA damage response and repair using laser microirradiation. Methods Cell Biol 2007, 82:377-407.
3. Kong X., Mohanty S.K., Stephens J., Heale J.T., Gomez-Godinez V., Shi L.Z., Kim J.S., Yokomori K., Berns M.W. Comparative analysis of different laser systems to study cellular responses to DNA damage in mammalian cells. Nucleic Acids Res 2009, 10.1093/nar/gkp221.
4. Sugawara N., Haber J.E. Repair of DNA double strand breaks: in vivo biochemistry. Methods Enzymol 2006, 408:416-429.
5. Kondo T., Wakayama T., Naiki T., Matsumoto K., Sugimoto K. Recruitment of Mec1 and Ddc1 checkpoint proteins to double-strand breaks through distinct mechanisms. Science 2001, 294:867-870.
6. Murr R., Loizou J.I., Yang Y.G., Cuenin C., Li H., Wang Z.Q., Herceg Z. Histone acetylation by Trrap-Tip60 modulates loading of repair proteins and repair of DNA double-strand breaks. Nat Cell Biol 2006, 8:91-99.
7. Melo J.A., Cohen J., Toczyski D.P. Two checkpoint complexes are independently recruited to sites of DNA damage in vivo. Genes Dev 2001, 15:2809-2821.
8. Berkovich E., Monnat R.J.J., Kastan M.B. Roles of ATM and NBS1 in chromatin structure modulation and DNA double-strand break repair. Nat Cell Biol 2007, 9:683-690.
9. Lukas C., Bartek J., Lukas J. Imaging of protein movement induced by chromosomal breakage: tiny 'local' lesions pose great 'global' challenges. Chromosoma 2005, 114:146-154.
10. Tobias F., Durante M., Taucher-Scholz G., Jakob B. Spatiotemporal analysis of DNA repair using charged particle radiation. Mutat Res 2010, 704:54-60.
11. Volker M., Moné M.J., Karmakar P., van Hoffen A., Schul W., Vermeulen W., Hoeijmakers J.H., van Driel R., van Zeeland A.A., Mullenders L.H. Sequential assembly of the nucleotide excision repair factors in vivo. Mol Cell 2001, 8:213-224.
12. Botchway S.W., Reynolds P., Parker A.W., O'Neill P. Use of near infrared femtosecond lasers as sub-micron radiation microbeam for cell DNA damage and repair studies. Mutat Res 2010, 704:38-44.
13. Muniandy P.A., Thapa D., Thazhathveetil A.K., Liu S.T., Seidman M.M. Repair of laser-localized DNA interstrand cross-links in G1 phase mammalian cells. J Biol Chem 2009, 284:27908-27917.
14. Ayoub N., Jeyasekharan A.D., Bernal J.A., Venkitaraman A.R. HP1-beta mobilization promotes chromatin changes that initiate the DNA damage response. Nature 2008, 453:682-686.
15. Luijsterburg M.S., Dinant C., Lans H., Stap J., Wiernasz E., Lagerwerf S., Warmerdam D.O., Lindh M., Brink M.C., Dobrucki J.W., et al. Heterochromatin protein 1 is recruited to various types of DNA damage. J Cell Biol 2009, 185:577-586.
16. Zarebski M., Wiernasz E., Dobrucki J.W. Recruitment of heterochromatin protein 1 to DNA repair sites. Cytometry 2009, 75:619-625.
17. Morris J.R., Boutell C., Keppler M., Densham R., Weekes D., Alamshah A., Butler L., Galanty Y., Pangon L., Kiuchi T., et al. The SUMO modification pathway is involved in the BRCA1 response to genotoxic stress. Nature 2009, 462:886-890.
18. Barlow J.H., Lisby M., Rothstein R. Differential regulation of the cellular response to DNA double-strand breaks in G1. Mol Cell 2008, 30:73-85.
19. Bradshaw P.S., Stavropoulos D.J., Meyn M.S. Human telomeric protein TRF2 associates with genomic double-strand breaks as an early response to DNA damage. Nat Genet 2005, 37:193-197.
20. Williams E.S., Stap J., Essers J., Ponnaiya B., Luijsterburg M.S., Krawczyk P.M., Ullrich R.L., Aten J.A., Bailey S.M. DNA double-strand breaks are not sufficient to initiate recruitment of TRF2. Nat Genet 2007, 39:696-698.
21. Splinter J., Jakob B., Lang M., Yano K., Engelhardt J., Hell S.W., Chen D.J., Durante M., Taucher-Scholz G. Biological dose estimation of UVA laser microirradiation utilizing charged particle-induced protein foci. Mutagenesis 2010, 25:289-297.
22. van Attikum H., Gasser S.M. The histone code at DNA breaks: a guide to repair?. Nat Rev Mol Cell Biol 2005, 6:757-765.
23. Kruhlak M.J., Celeste A., Dellaire G., Fernandez-Capetillo O., Müller W.G., McNally J.G., Bazett-Jones D.P., Nussenzweig A. Changes in chromatin structure and mobility in living cells at sites of DNA double-strand breaks. J Cell Biol 2006, 172:823-834.
24. Goodarzi A.A., Noon A.T., Deckbar D., Ziv Y., Shiloh Y., Löbrich M., Jeggo P.A. ATM signaling facilitates repair of DNA double-strand breaks associated with heterochromatin. Mol Cell 2008, 31:167-177.
25. Ziv Y., Bielopolski D., Galanty Y., Lukas C., Taya Y., Schultz D.C., Lukas J., Bekker-Jensen S., Bartek J., Shiloh Y. 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.
26. Huber A., Bai P., de Murcia J.M., de Murcia G. PARP-1, PARP-2 and ATM in the DNA damage response: functional synergy in mouse development. DNA Repair 2004, 3:1103-1108.
27. Iliakis G. Backup pathways of NHEJ in cells of higher eukaryotes: cell cycle dependence. Radiother Oncol 2009, 92:310-315.
28. Krishnakumar R., Kraus W.L. The PARP side of the nucleus: molecular actions, physiological outcomes, and clinical targets. Mol Cell 2010, 39:8-24.
29. Mortusewicz O., Amé J.C., Schreiber V., Leonhardt H. Feedback-regulated poly(ADP-ribosyl)ation by PARP-1 is required for rapid response to DNA damage in living cells. Nucleic Acids Res 2007, 35:7665-7675.
30. Kim J.-S., Krasieva T.B., LaMorte V.J., Taylor A.M.R., Yokomori K. Specific recruitment of human cohesin to laser-induced DNA damage. J Biol Chem 2002, 277:45149-45153.
31. Lan L., Nakajima S., Oohata Y., Takao M., Okano S., Masutani M., Wilson S.H., Yasui A. In situ analysis of repair processes for oxidative DNA damage in mammalian cells. Proc Natl Acad Sci 2004, 101:13738-13743.
32. Ueda K., Omachi A., Kawaichi M., Hayaishi O. Natural occurrence of poly(ADP-ribosyl) histones in rat liver. Proc Natl Acad Sci 1975, 72:205-209.
33. Poirier G., de Murcia G., Jongstra-Bilen J., Niedergang C., Mandel P. Poly(ADP-ribosyl)ation of polynucleosomes causes relaxation of chromatin structure. Proc Natl Acad Sci 1982, 79:3423-3427.
34. Wacker D.A., Ruhl D.D., Balagamwala E.H., Hope K.M., Zhang T., Kraus W.L. The DNA binding and catalytic domains of poly(ADP-ribose) polymerase 1 cooperate in the regulation of chromatin structure and transcription. Mol Cell Biol 2007, 27:7475-7485.
35. Tulin A., Spradling A. Chromatin loosening by poly(ADP)-ribose polymerase (PARP) at Drosophila puff loci. Science 2003, 299:560-562.
36. Ahel I., Ahel D., Matsusaka T., Clark A.J., Pines J., Boulton S.J., West S.C. Poly(ADP-ribose)-binding zinc finger motifs in DNA repair/checkpoint proteins. Nature 2008, 451:81-85.
37. Ahel D., Horejsí Z., Wiechens N., Polo S.E., Garcia-Wilson E., Ahel I., Flynn H., Skehel M., West S.C., Jackson S.P., et al. Poly(ADP-ribose)-dependent regulation of DNA repair by the chromatin remodeling enzyme ALC1. Science 2009, 325:1240-1243.
38. Gottschalk A.J., Timinszky G., Kong S.E., Jin J., Cai Y., Swanson S.K., Washburn M.P., Florens L., Ladurner A.G., Conaway J.W., et al. Poly(ADP-ribosyl)ation directs recruitment and activation of an ATP-dependent chromatin remodeler. Proc Natl Acad Sci 2009, 106:13770-13774.
39. Ramírez J., Hagman J. The Mi-2/NuRD complex: a critical epigenetic regulator of hematopoietic development, differentiation and cancer. Epigenetics 2009, 4:532-536.
40. Chou D.M., Adamson B., Dephoure N.E., Tan X., Nottke A.C., Hurov K.E., Gygi S.P., Colaiácovo M.P., Elledge S.J. A chromatin localization screen reveals poly (ADP ribose)-regulated recruitment of the repressive polycomb and NuRD complexes to sites of DNA damage. Proc Natl Acad Sci 2010, 107:18475-18480.
41. Larsen D.H., Poinsignon C., Gudjonsson T., Dinant C., Payne M.R., Hari F.J., Danielsen J.M., Menard P., Sand J.C., Stucki M., et al. The chromatin-remodeling factor CHD4 coordinates signaling and repair after DNA damage. J Cell Biol 2010, 190:731-740.
42. Polo S.E., Kaidi A., Baskcomb L., Galanty Y., Jackson S.P. Regulation of DNA-damage responses and cell-cycle progression by the chromatin remodelling factor CHD4. EMBO J 2010, 29:3130-3139.
43. Smeenk G., Wiegant W.W., Vrolijk H., Solari A.P., Pastink A., van Attikum H. The NuRD chromatin-remodeling complex regulates signaling and repair of DNA damage. J Cell Biol 2010, 190:741-749.
44. Timinszky G., Till S., Hassa P.O., Hothorn M., Kustatscher G., Nijmeijer B., Colombelli J., Altmeyer M., Stelzer E.H., Scheffzek K., et al. A macrodomain-containing histone rearranges chromatin upon sensing PARP1 activation. Nat Struct Mol Biol 2009, 16:923-929.
45. Cao R., Tsukada Y., Zhang Y. Role of Bmi-1 and Ring1A in H2A ubiquitylation and Hox gene silencing. Mol Cell 2005, 20:845-854.
46. Cao R., Wang L., Wang H., Xia L., Erdjument-Bromage H., Tempst P., Jones R.S., Zhang Y. Role of histone H3 lysine 27 methylation in Polycomb-group silencing. Science 2002, 298:1039-1043.
47. Morey L., Helin K. Polycomb group protein-mediated repression of transcription. Trends Biochem Sci 2010, 35:323-332.
48. Ismail I.H., Andrin C., McDonald D., Hendzel M.J. BMI1-mediated histone ubiquitylation promotes DNA double-strand break repair. J Cell Biol 2010, 191:45-60.
49. Ladurner A.G. Inactivating chromosomes: a macro domain that minimizes transcription. Mol Cell 2003, 12:1-3.
50. Miller K.M., Tjeertes J.V., Coates J., Legube G., Polo S.E., Britton S., Jackson S.P. Human HDAC1 and HDAC2 function in the DNA-damage response to promote DNA nonhomologous end-joining. Nat Struct Mol Biol 2010, 17:1144-1151.
51. Eissenberg J.C., James T.C., Foster-Hartnett D.M., Hartnett T., Ngan V., Elgin S.C.R. Mutation in a heterochromatin-specific chromosomal protein is associated with suppression of position-effect variegation in Drosophiola melanogaster. Proc Natl Acad Sci USA 1990, 87:9923-9927.
52. Kim J.-S., Krasieva T.B., Kurumizaka H., Chen D.J., Taylor A.M., Yokomori K. Independent and sequential recruitment of NHEJ and HR factors to DNA damage sites in mammalian cells. J Cell Biol 2005, 170:341-347.
53. Frank-Vaillant M., Marcand S. Transient stability of DNA ends allows nonhomologous end joining to precede homologous recombination. Mol Cell 2002, 10:1189-1199.
54. Delacote F., Han M., Stamato T.D., Jasin M., Lopez B.S. An XRCC4 defect or Wortmannin stimulates homologous recombination specifically induced by double-strand breaks in mammalian cells. Nucleic Acids Res 2002, 30:3454-3463.
55. Galanty Y., Belotserkovskaya R., Coates J., Polo S., Miller K.M., Jackson S.P. Mammalian SUMO E3-ligases PIAS1 and PIAS4 promote responses to DNA double-strand breaks. Nature 2009, 462:935-939.
56. Rouleau M., Patel A., Hendzel M.J., Kaufmann S.H., Poirier G.G. PARP inhibition: PARP1 and beyond. Nat Rev Cancer 2010, 10:293-301.
57. Tan J., Cang S., Ma Y., Petrillo R.L., Liu D. Novel histone deacetylase inhibitors in clinical trials as anti-cancer agents. J Hematol Oncol 2010, 3:5.
58. Redon C.E., Nakamura A.J., Zhang Y.W., Ji J.J., Bonner W.M., Kinders R.J., Parchment R.E., Doroshow J.H., Pommier Y. Histone gammaH2AX and poly(ADP-ribose) as clinical pharmacodynamic biomarkers. Clin Cancer Res 2010, 16:4532-4542.