De novo nucleosome assembly: New pieces in an old puzzle

Genes and Development

Volumn 14, Issue 12, 2000, Pages 1430-1438

  Verreault, Alain ^a  

^a IMPERIAL CANCER RESEARCH FUND   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

HISTONE;

ACETYLATION; CHROMATIN; DNA REPLICATION; NONHUMAN; NUCLEOSOME; PRIORITY JOURNAL; PROTEIN DNA INTERACTION; REVIEW;

ACETYLATION; CELL CYCLE; CHROMOSOMES; DNA; DNA REPAIR; EUKARYOTIC CELLS; HISTONES; MODELS, BIOLOGICAL; NUCLEOSOMES; SACCHAROMYCES CEREVISIAE;

EID: 0034659231     PISSN: 08909369     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Review

References (76)

1. Altheim, B.A. and M.C. Schultz. 1999. Histone modification governs the cell cycle regulation of a replication-independent chromatin assembly pathway in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. 96: 1345-1350.
2. Altman, R. and D. Kellogg. 1997. Control of mitotic events by Nap1 and the Gin4 kinase. J. Cell. Biol. 138: 119-130.
3. Chang, L., S.S. Loranger, C. Mizzen, S.G. Ernst, C.D. Allis, and A.T. Annunziato. 1997. Histones in transit: Cytosolic histone complexes and diacetylation of H4 during nucleosome assembly in human cells. Biochemistry 36: 469-480.
4. Chuang, L.S., H.I. Ian, T.W. Koh, H.H. Ng, G. Xu, and B.F. Li. 1997. Human DNA-(cytosine-5) methyltransferase-PCNA complex as a target for p21WAF1. Science 277: 1996-2000.
5. Corona, D.F., G. Langst, C.R. Clapier, E.J. Bonte, S. Ferrari, J.W. Tamkun, and P.B. Becker. 1999. ISWI is an ATP-dependent nucleosome remodeling factor. Mol. Cell 3: 239-245.
6. Covault, J. and R. Chalkley. 1980. The identification of distinct populations of acetylated histone. J. Biol. Chem. 255: 9110-9116.
7. Davie, J.R., C.A. Saunders, J.M. Walsh, and S.C. Weber. 1981. Histone modifications in the yeast S. cerevisiae. Nucleic Acids Res. 9: 3205-3216.
8. Dilworth, S.M. and C. Dingwall. 1988. Chromatin assembly in vitro and in vivo. BioEssays 9: 44-49.
9. Ekwall, K., T. Olsson, B.M. Turner, G. Cranston, and R.C. Allshire. 1997. Transient inhibition of histone deacetylation alters the structural and functional imprint at fission yeast centromeres. Cell 91: 1021-1032.
10. Enomoto, S. and J. Berman. 1998. Chromatin assembly factor-1 contributes to the maintenance, but not the re-establishment, of silencing at the yeast silent mating loci. Genes & Dev. 12: 219-232.
11. Enomoto, S., P.D. McCune-Zierath, M. Gerami-Nejad, M.A. Sanders, and J. Berman. 1997. RLF2, a subunit of yeast chromatin assembly factor-1, is required for telomeric chromatin function in vivo. Genes & Dev. 11: 358-370.
12. Fuks, F., W.A. Burgers, A. Brehm, L. Hughes-Davies, and T. Kouzarides. 2000. DNA methyltransferase Dnmt1 associates with histone deacetylase activity. Nat. Genet. 24: 88-91.
13. Gaillard, P.H., E.M. Martini, P.D. Kaufman, B. Stillman, E. Moustacchi, and G. Almouzni. 1996. Chromatin assembly coupled to DNA repair: A new role for chromatin assembly factor 1. Cell 86: 887-896.
14. Game, J.C. and P.D. Kaufman. 1999. Role of Saccharomyces cerevisiae chromatin assembly factor-1 in repair of ultraviolet radiation damage in vivo. Genetics 151: 485-497.
15. Glikin, G.C., I. Ruberti, and A. Worcel. 1984. Chromatin assembly in Xenopus oocytes: In vitro studies. Cell 37: 33-41.
16. Grewal, S.I., M.J. Bonaduce, and A.J. Klar. 1998. Histone deacetylase homologs regulate epigenetic inheritance of transcriptional silencing and chromosome segregation in fission yeast. Genetics 150: 563-576.
17. Hendrich, B. and A. Bird. 1998. Identification and characterization of a family of mammalian methyl-CpG binding proteins. Mol. Cell. Biol. 18: 6538-6547.
18. Imhof, A. and A.P. Wolffe. 1999. Purification and properties of the Xenopus Hat1 acetyltransferase: Association with the 14-3-3 proteins in the oocyte nucleus. Biochemistry 38: 13085-13093.
19. Ishimi, Y. and A. Kikuchi. 1991. Identification and molecular cloning of yeast homolog of nucleosome assembly protein 1 which facilitates nucleosome assembly in vitro. J. Biol. Chem. 266: 7025-7029.
20. Ito, T., M. Bulger, R. Kohayashi, and J.T. Kadonaga. 1996a. Drosophila NAP-1 is a core histone chaperone that functions in ATP-facilitated assembly of regularly spaced nucleosomal arrays. Mol. Cell. Biol. 16: 3112-3124.
21. Ito, T., J.K. Tyler, M. Bulger, R. Kobayashi, and J.T. Kadonaga. 1996b. ATP-facilitated chromatin assembly with a nucleoplasmin-like protein from Drosophila melanogaster. J. Biol. Chem. 271: 25041-25048.
22. Ito, T., M. Bulger, M.J. Pazin, R. Kobayashi, and J.T. Kadonaga. 1997a. ACF, an ISWI-containing and ATP-utilizing chromatin assembly and remodeling factor. Cell 90: 145-155.
23. Ito, T., J.K. Tyler, and J.T. Kadonaga. 1997b. Chromatin assembly factors: A dual function in nucleosome formation and mobilization? Genes Cells 2: 593-600.
24. Ito, T., M.E. Levenstein, D.V. Fyodorov, A.K. Kutach, R. Kobayashi, and J.T. Kadonaga. 1999. ACF consists of two subunits, Acf1 and ISWI, that function cooperatively in the ATP-dependent catalysis of chromatin assembly. Genes & Dev. 13: 1529-1539.
25. Jackson, V., A. Shires, N. Tanphaichitr, and R. Chalkley. 1976. Modifications to histones immediately after synthesis. J. Mol. Biol. 104: 471-483.
26. Jones, P.L., G.J. Veenstra, P.A. Wade, D. Vermaak, S.U. Kass, N. Landsberger, J. Strouboulis, and A.P. Wolffe. 1998. Methylated DNA and MeCP2 recruit histone deacetylase to repress transcription. Nat. Genet. 19: 187-191.
27. Jonsson, Z.O. and U. Hubscher. 1997. Proliferating cell nuclear antigen: More than a clamp for DNA polymerases. BioEssays 19: 967-975.
28. Kamakaka, R.T., M. Bulger, and J.T. Kadonaga. 1993. Potentiation of RNA polymerase II transcription by Ga14-VP16 during but not after DNA replication and chromatin assembly. Genes & Dev. 7: 1779-1795.
29. Kaufman, P.D., R. Kobayashi, and B. Stillman. 1997. Ultraviolet radiation sensitivity and reduction of telomeric silencing in Saccharomyces cerevisiae cells lacking chromatin assembly factor-1. Genes & Dev. 11: 345-357.
30. Kaufman, P.D., J.L. Cohen, and M.A. Osley. 1998. Hir proteins are required for position-dependent gene silencing in Saccharomyces cerevisiae in the absence of chromatin assembly factor 1. Mol. Cell. Biol. 18: 4793-4806.
31. Kim, U.J., M. Han, P. Kayne, and M. Grunstein. 1988. Effects of histone H4 depletion on the cell cycle and transcription of Saccharomyces cerevisiae. EMBO J. 7: 2211-2219.
32. Kleff, S., E.D. Andrulis, C.W. Anderson, and R. Sternglanz. 1995. Identification of a gene encoding a yeast histone H4 acetyltransferase. J. Biol. Chem. 270: 24674-24677.
33. Krude, T. 1995. Chromatin assembly factor-1 (CAF-1) colocalizes with replication foci in HeLa cell nuclei. Exp. Cell. Res. 220: 304-311.
34. _. 1999. Chromatin assembly during DNA replication in somatic cells. Eur. J. Biochem. 263: 1-5.
35. Kuo, M.H., J.E. Brownell, R.E. Sobel, T.A. Ranalli, R.G. Cook, D.G. Edmondson, S.Y. Roth, and C.D. Allis. 1996. Transcription-linked acetylation by Gen5p of histones H3 and H4 at specific lysines. Nature 383: 269-272.
36. Lamour, V., Y. Lecluse, C. Desmaze, M. Spector, M. Bodescot, A. Aurias, M.A. Osley, and M. Lipinski. 1995. A human homolog of the S. cerevisiae HIR1 and HIR2 transcriptional repressors cloned from the DiGeorge syndrome critical region. Hum. Mol. Genet. 4: 791-799.
37. Le, S., C. Davis, J.B. Konopka, and R. Sternglanz. 1997. Two new S-phase-specific genes from Saccharomyces cerevisiae. Yeast 13: 1029-1042.
38. LeRoy, G., G. Orphanides, W.S. Lane, and D. Reinberg. 1998. Requirement of RSF and FACT for transcription of chromatin templates in vitro. Science 282: 1900-1904.
39. Lindahl, T. and R.D. Wood. 1999. Quality control by DNA repair. Science 286: 1897-1905.
40. Ling, X., T.A. Harkness, M.C. Schultz, G. Fisher-Adams, and M. Grunstein. 1996. Yeast histone H3 and H4 amino termini are important for nucleosome assembly in vivo and in vitro: Redundant and position-independent functions in assembly but not in gene regulation. Genes & Dev. 10: 686-699.
41. Lorain, S., J.P. Quivy, F. Monier-Gavelle, C. Scamps, Y. Lecluse, G. Almouzni, and M. Lipinski. 1998. Core histones and HI-RIP3, a novel histone-binding protein, directly interact with WD repeat protein HIRA. Mol. Cell. Biol. 18: 5546-5556.
42. Ma, X.J., J. Wu, B.A. Altheim, M.C. Schultz, and M. Grunstein. 1998. Deposition-related sites K5/K12 in histone H4 are not required for nucleosome deposition in yeast. Proc. Natl. Acad. Sci. 95: 6693-6698.
43. Martinez-Balbas, M.A., U.M. Bauer, S.J. Nielsen, A. Brehm, and T. Kouzarides. 2000. Regulation of E2F1 activity by acetylation. EMBO J. 19: 662-671.
44. Martini, E., D.M. Roche, K. Marheineke, A. Verreault, and G. Almouzni. 1998. Recruitment of phosphorylated chromatin assembly factor 1 to chromatin after UV irradiation of human cells. J. Cell. Biol. 143: 563-575.
45. Megee, P.C., B.A. Morgan, and M.M. Smith. 1995. Histone H4 and the maintenance of genome integrity. Genes & Dev. 9: 1716-1727.
46. Moggs, J.G. and G. Almouzni. 1999. Chromatin rearrangements during nucleotide excision repair. Biochimie 81: 45-52.
47. Moggs, J.G., P. Grandi, J.P. Quivy, Z.O. Jonsson, U. Hubscher, P.B. Becker, and G. Almouzni. 2000. A CAF-1-PCNA-mediated chromatin assembly pathway triggered by sensing DNA damage. Mol. Cell. Biol. 20: 1206-1218.
48. Monson, E.K., D. de Bruin, and V.A. Zakian. 1997. The yeast Cac1 protein is required for the stable inheritance of transcriptionally repressed chromatin at telomeres. Proc. Natl. Acad. Sci. 94: 13081-13086.
49. Moran, L., D. Norris, and M.A. Osley. 1990. A yeast H2A-H2B promoter can be regulated by changes in histone gene copy number. Genes & Dev. 4: 752-763.
50. Nan, X., P. Tate, E. Li, and A. Bird. 1996. DNA methylation specifies chromosomal localization of MeCP2. Mol. Cell. Biol. 16: 414-421.
51. Nan, X., H.H. Ng, C.A. Johnson, C.D. Laherty, B.M. Turner, R.N. Eisenman, and A. Bird. 1998. Transcriptional repression by the methyl-CpG-binding protein MeCP2 involves a histone deacetylase complex. Nature 393: 386-389.
52. Ng, H.H., Y. Zhang, B. Hendrich, C.A. Johnson, B.M. Turner, H. Erdjument-Bromage, P. Tempst, D. Reinberg, and A. Bird. 1999. MBD2 is a transcriptional repressor belonging to the MeCP1 histone deacetylase complex. Nat. Genet. 23: 58-61.
53. Osley, M.A. and D. Lycan. 1987. Trans-acting regulatory mutations that alter transcription of Saccharomyces cerevisiae histone genes. Mol. Cell. Biol. 7: 4204-4210.
54. Parthun, M.R., J. Widom, and D.E. Gottschling. 1996. The major cytoplasmic histone acetyltransferase in yeast: Links to chromatin replication and histone metabolism. Cell 87: 85-94.
55. Qian, Z., H. Huang, J.Y. Hong, C.L. Burck, S.D. Johnston, J. Berman, A. Carol, and S.W. Liebman. 1998. Yeast Ty1 retrotransposition is stimulated by a synergistic interaction between mutations in chromatin assembly factor 1 and histone regulatory proteins. Mol. Cell. Biol. 18: 4783-4792.
56. Rodriguez, P., J. Pelletier, G.B. Price, and M. Zannis-Hadjopoulos. 2000. NAP-2: Histone chaperone function and phosphorylation state through the cell cycle. J. Mol. Biol. 298: 225-238.
57. Roth, S.Y. and C.D. Allis. 1996. Histone acetylation and chromatin assembly: A single escort, multiple dances? Cell 87: 5-8.
58. Rundlett, S.E., A.A. Carmen, R. Kobayashi, S. Bavykin, B.M. Turner, and M. Grunstein. 1996. HDA1 and RPD3 are members of distinct yeast histone deacetylase complexes that regulate silencing and transcription. Proc. Natl. Acad. Sci. 93: 14503-14508.
59. Sherwood, P.W., S.V. Tsang, and M.A. Osley. 1993. Characterization of HIR1 and HIR2, two genes required for regulation of histone gene transcription in Saccharomyces cerevisiae. Mol. Cell. Biol. 13: 28-38.
60. Shibahara, K. and B. Stillman. 1999. Replication-dependent marking of DNA by PCNA facilitates CAF-1-coupled inheritance of chromatin. Cell 96: 575-585.
61. Shibahara, K.S., A. Verreault, and B. Stillman. 2000. The N-tcrminal domains of histones H3 and H4 are not necessary for chromatin assembly factor 1-mediated nucleosome assembly onto replicated DNA in vitro. Proc. Natl. Acad. Sci. (in press).
62. Singer, M.S., A. Kahana, A.J. Wolf, L.L. Meisinger, S.E. Peterson, C. Goggin, M. Mahowald, and D.E. Gottschling. 1998. Identification of high-copy disruptors of telomeric silencing in Saccharomyces cerevisiae. Genetics 150: 613-632.
63. Smith, S. and B. Stillman. 1989. Purification and characterization of CAF-1, a human cell factor required for chromatin assembly during DNA replication. Cell 58: 15-25.
64. _. 1991. Stepwise assembly of chromatin during DNA replication in vitro. EMBO J. 10: 971-980.
65. Sobel, R.E., R.G. Cook, C.A. Perry, A.T. Annunziato, and C.D. Allis. 1995. Conservation of deposition-related acetylation sites in newly synthesized histones H3 and H4. Proc. Natl. Acad. Sci. 92: 1237-1241.
66. Taddei, A., D. Roche, J.B. Sibarita, B.M. Turner, and G. Almouzni. 1999. Duplication and maintenance of heterochromatin domains. J. Cell. Biol. 147: 1153-1166.
67. Torres-Ramos, C.A., B.L. Yoder, P.M. Burgers, S. Prakash, and L. Prakash. 1996. Requirement of proliferating cell nuclear antigen in RAD6-dependent postreplicational DNA repair. Proc. Natl. Acad. Sci. 93: 9676-9681.
68. Tsukiyama, T. and C. Wu. 1995. Purification and properties of an ATP-dependent nucleosome remodeling factor. Cell 83: 1011-1020.
69. Tyler, J.K., C.R. Adams, S.R. Chen, R. Kobayashi, R.T. Kamakaka, and J.T. Kadonaga. 1999. The RCAF complex mediates chromatin assembly during DNA replication and repair. Nature 402: 555-560.
70. Varga-Weisz, P.D., M. Wilm, E. Bonte, K. Dumas, M. Mann, and P.B. Becker. 1997. Chromatin-remodelling factor CHRAC contains the ATPases ISWI and topoisomerase II. Nature 388: 598-602.
71. Verreault, A., P.D. Kaufman, R. Kobayashi, and B. Stillman. 1996. Nucleosome assembly by a complex of CAF-1 and acetylated histones H3/H4. Cell 87: 95-104.
72. _. 1998. Nucleosomal DNA regulates the core-histone-binding subunit of the human Hat1 acetyltransferase. Curr. Biol. 8: 96-108.
73. Vignali, M., A.H. Hassan, K.E. Neely, and J.L. Workman. 2000. ATP-dependent chromatin-remodeling complexes. Mol. Cell. Biol. 20: 1899-1910.
74. Wilming, L.G., C.A. Snoeren, A. van Rijswijk, F. Grosveld, and C. Meijers. 1997. The murine homologue of HIRA, a Di-George syndrome candidate gene, is expressed in embryonic structures affected in human CATCH22 patients. Hum. Mol. Genet. 6: 247-258.
75. Worcel, A., S. Han, and M.L. Wong. 1978. Assembly of newly replicated chromatin. Cell 15: 969-977.
76. Zhang, D.E. and D.A. Nelson. 1988. Histone acetylation in chicken erythrocytes. Rates of acetylation and evidence that histones in both active and potentially active chromatin are rapidly modified. Biochem. J. 250: 233-240.