Methods for Studying Chromatin Assembly Coupled to DNA Repair

Methods in Enzymology

Volumn 409, Issue , 2006, Pages 358-374

  Gérard, Annabelle ^a   Polo, Sophie E ^a   Roche, Danièle ^a   Almouzni, Geneviève ^a  

^a NONE

Author keywords

[No Author keywords available]

Indexed keywords

CIRCULAR DNA; HISTONE;

CELL FREE SYSTEM; CELL NUCLEUS; CHROMATIN ASSEMBLY AND DISASSEMBLY; CONTROLLED STUDY; DNA DAMAGE; DNA REPAIR; DNA SUPERCOILING; HUMAN; HUMAN CELL; NUCLEOSOME; PLASMID; PRIORITY JOURNAL; PROTEIN INTERACTION; REVIEW;

CELL LINE; CHROMATIN; DNA REPAIR; HUMANS; NUCLEOSOMES; PLASMIDS; ULTRAVIOLET RAYS;

EUKARYOTA;

EID: 33745212870     PISSN: 00766879     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S0076-6879(05)09021-X     Document Type: Review

References (38)

1. Almouzni G. "Chromatin: A practical approach," (1998), Oxford University Press, New York 195-218
2. Bonte E., and Becker P.B. Preparation of chromatin assembly extracts from preblastoderm Drosophila embryos. Methods Mol. Biol. 119 (1999) 187-194
3. Bradford M.M. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal. Biochem. 72 (1976) 248-254
4. Brand M., Moggs J.G., Oulad-Abdelghani M., Lejeune F., Dilworth F.J., Stevenin J., Almouzni G., and Tora L. UV-damaged DNA-binding protein in the TFTC complex links DNA damage recognition to nucleosome acetylation. EMBO J. 20 (2001) 3187-3196
5. Dignam J.D., Lebovitz R.M., and Roeder R.G. Accurate transcription initiation by RNA polymerase II in a soluble extract from isolated mammalian nuclei. Nucleic Acids Res. 11 (1983) 1475-1489
6. Gaillard P.H., Martini E.M., Kaufman P.D., Stillman B., Moustacchi E., and Almouzni G. Chromatin assembly coupled to DNA repair: A new role for chromatin assembly factor I. Cell 86 (1996) 887-896
7. Gaillard P.H., Moggs J.G., Roche D.M., Quivy J.P., Becker P.B., Wood R.D., and Almouzni G. Initiation and bidirectional propagation of chromatin assembly from a target site for nucleotide excision repair. EMBO J. 16 (1997) 6281-6289
8. Gaillard P.H., Roche D., and Almouzni G. Nucleotide excision repair coupled to chromatin assembly. Methods Mol. Biol. 119 (1999) 231-243
9. Green C.M., and Almouzni G. When repair meets chromatin. First in series on chromatin dynamics. EMBO Rep. 3 (2002) 28-33
10. Green C.M., and Almouzni G. Local action of the chromatin assembly factor CAF-1 at sites of nucleotide excision repair in vivo. EMBO J. 22 (2003) 5163-5174
11. Groth A., Ray-Gallet D., Quivy J.P., Lukas J., Bartek J., and Almouzni G. Human Asf1 regulates the flow of S phase histones during replicational stress. Mol. Cell 17 (2005) 301-311
12. Hoek M., and Stillman B. Chromatin assembly factor 1 is essential and couples chromatin assembly to DNA replication in vivo. Proc. Natl. Acad. Sci. USA 100 (2003) 12183-12188
13. Kaufman P.D., Kobayashi R., Kessler N., and Stillman B. The p150 and p60 subunits of chromatin assembly factor I: A molecular link between newly synthesized histones and DNA replication. Cell 81 (1995) 1105-1114
14. Kornberg R.D. Structure of chromatin. Annu. Rev. Biochem. 46 (1977) 931-954
15. Krude T., Jackman M., Pines J., and Laskey R.A. Cyclin/Cdk-dependent initiation of DNA replication in a human cell-free system. Cell 88 (1997) 109-119
16. Li J.J., and Kelly T.J. Simian virus 40 DNA replication in vitro. Proc. Natl. Acad. Sci. USA 81 (1984) 6973-6977
17. Loyola A., and Almouzni G. Histone chaperones, a supporting role in the limelight. Biochim. Biophys. Acta 1677 (2004) 3-11
18. Lukas C., Falck J., Bartkova J., Bartek J., and Lukas J. Distinct spatiotemporal dynamics of mammalian checkpoint regulators induced by DNA damage. Nat. Cell. Biol. 5 (2003) 255-260
19. Marheineke K., and Krude T. Nucleosome assembly activity and intracellular localization of human CAF-1 changes during the cell division cycle. J. Biol. Chem. 273 (1998) 15279-15286
20. Martini E., Roche D.M., Marheineke K., Verreault A., and Almouzni G. Recruitment of phosphorylated chromatin assembly factor 1 to chromatin after UV irradiation of human cells. J. Cell. Biol. 143 (1998) 563-575
21. Mello J.A., and Almouzni G. The ins and outs of nucleosome assembly. Curr. Opin. Genet. Dev. 11 (2001) 136-141
22. Mello J.A., Moggs J.G., and Almouzni G. Analysis of DNA repair and chromatin assembly in vitro using immobilized damaged DNA substrates. Methods Mol. Biol. 281 (2004) 271-281
23. Moggs J.G., and Almouzni G. Assays for chromatin remodeling during DNA repair. Methods Enzymol. 304 (1999) 333-351
24. Moggs J.G., Grandi P., Quivy J.P., Jonsson Z.O., Hubscher U., Becker P.B., and Almouzni G. A CAF-1-PCNA-mediated chromatin assembly pathway triggered by sensing DNA damage. Mol. Cell. Biol. 20 (2000) 1206-1218
25. Mone M.J., Volker M., Nikaido O., Mullenders L.H., van Zeeland A.A., Verschure P.J., Manders E.M., and van Driel R. Local UV-induced DNA damage in cell nuclei results in local transcription inhibition. EMBO Rep. 2 (2001) 1013-1017
26. Nabatiyan A., and Krude T. Silencing of chromatin assembly factor 1 in human cells leads to cell death and loss of chromatin assembly during DNA synthesis. Mol. Cell. Biol. 24 (2004) 2853-2862
27. Okano S., Lan L., Caldecott K.W., Mori T., and Yasui A. Spatial and temporal cellular responses to single-strand breaks in human cells. Mol. Cell. Biol. 23 (2003) 3974-3981
28. Quivy J.P., Grandi P., and Almouzni G. Dimerization of the largest subunit of chromatin assembly factor 1: Importance in vitro and during Xenopus early development. EMBO J. 20 (2001) 2015-2027
29. Ray-Gallet D., and Almouzni G. DNA synthesis-dependent and -independent chromatin assembly pathways in Xenopus egg extracts. Methods Enzymol. 375 (2004) 117-131
30. Rogakou E.P., Boon C., Redon C., and Bonner W.M. Megabase chromatin domains involved in DNA double-strand breaks in vivo. J. Cell. Biol. 146 (1999) 905-916
31. Shibahara K., and Stillman B. Replication-dependent marking of DNA by PCNA facilitates CAF-1-coupled inheritance of chromatin. Cell 96 (1999) 575-585
32. Smerdon M.J., and Lieberman M.W. Nucleosome rearrangement in human chromatin during UV-induced DNA-repair synthesis. Proc. Natl. Acad. Sci. USA 75 (1978) 4238-4241
33. Smith S., and Stillman B. Purification and characterization of CAF-I, a human cell factor required for chromatin assembly during DNA replication in vitro. Cell 58 (1989) 15-25
34. Stillman B. Chromatin assembly during SV40 DNA replication in vitro. Cell 45 (1986) 555-565
35. Stillman B.W., and Gluzman Y. Replication and supercoiling of simian virus 40 DNA in cell extracts from human cells. Mol. Cell. Biol. 5 (1985) 2051-2060
36. Tagami H., Ray-Gallet D., Almouzni G., and Nakatani Y. Histone h3.1 and h3.3 complexes mediate nucleosome assembly pathways dependent or independent of DNA synthesis. Cell 116 (2004) 51-61
37. Vaquero A., Loyola A., and Reinberg D. The constantly changing face of chromatin. Sci. Aging Knowledge Environ. 2003 (2003) RE4
38. Wassarman P.M., and Kornberg R.D. "Nucleosomes." (1989), Academic Press, Inc., San Diego, CA