The roles of chromatin remodelling factors in replication

Results and Problems in Cell Differentiation

Volumn 41, Issue , 2006, Pages 91-107

  Neves Costa, Ana ^a   Varga Weisz, Patrick ^a  

^a BABRAHAM INSTITUTE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE TRIPHOSPHATASE; ADENOSINE TRIPHOSPHATE; CHAPERONE; HISTONE; ISWI PROTEIN; TRANSCRIPTION FACTOR;

ANIMAL; ARTICLE; CHROMATIN ASSEMBLY AND DISASSEMBLY; DNA REPLICATION; HUMAN; METABOLISM; PHYSIOLOGY;

ADENOSINE TRIPHOSPHATASES; ADENOSINE TRIPHOSPHATE; ANIMALS; CHROMATIN ASSEMBLY AND DISASSEMBLY; DNA REPLICATION; HISTONES; HUMANS; MOLECULAR CHAPERONES; TRANSCRIPTION FACTORS;

EID: 33845265264     PISSN: 00801844     EISSN: 18610412     Source Type: Book Series    
DOI: 10.1007/400_007     Document Type: Article

References (106)

1. Akey CW, Luger K (2003) Histone chaperones and nucleosome assembly. Curr Opin Struct Biol 13:6-14
2. Alexeev A, Mazin A, Kowalczykowski SC (2003) Rad54 protein possesses chromatinremodeling activity stimulated by the Rad51-ssDNA nucleoprotein filament. Nat Struct Biol 10:182-186
3. Alexiadis V, Lusser A, Kadonaga JT (2004) A conserved N-terminal motif in Rad54 is important for chromatin remodeling and homologous strand pairing. J Biol Chem 279:27824-27829
4. Alexiadis V, Varga-Weisz PD, Bonte E, Becker PB, Gruss C (1998) In vitro chromatin remodelling by chromatin accessibility complex (CHRAC) at the SV40 origin of DNA replication. Embo J 17:3428-3438
5. Aligianni S, Varga-Weisz P (2005) Chromatin-remodelling factors and the maintenance of transcriptional states through DNA replication. Biochem Soc Symp 73:97-108
6. Anderson LA, Perkins ND (2002) The large subunit of replication factor C interacts with the histone deacetylase, HDAC1. J Biol Chem 277:29550-29554
7. Annunziato AT (2005) Split decision: What happens to nucleosomes during DNA replication? J Biol Chem 280:12065-12068
8. Aparicio JG, Viggiani CJ, Gibson DG, Aparicio OM (2004) The Rpd3-Sin3 histone deacetylase regulates replication timing and enables intra-S origin control in Saccharomyces cerevisiae. Mol Cell Biol 24:4769-4780
9. Baetz KK, Krogan NJ, Emili A, Greenblatt J, Hieter P (2004) The ctf13-30/ CTF13 genomic haploinsufficiency modifier screen identifies the yeast chromatin remodeling complex RSC, which is required for the establishment of sister chromatid cohesion. Mol Cell Biol 24:1232-1244
10. Banting GS, Barak O, Ames TM, Burnham AC, Kardel MD, Cooch NS, Davidson CE, Godbout R, McDermid HE, Shiekhattar R (2005) CECR2, a protein involved in neurulation, forms a novel chromatin remodeling complex with SNF2L. Hum Mol Genet 14:513-524
11. Barak O, Lazzaro MA, Lane WS, Speicher DW, Picketts DJ, Shiekhattar R (2003) Isolation of human NURF: A regulator of Engrailed gene expression. Embo J 22:6089-6100
12. Becker PB (2005) Nucleosome remodelers on track. Nat Struct Mol Biol 12:732-733
13. Becker PB, Horz W (2002) ATP-dependent nucleosome remodeling. Annu Rev Biochem 71:247-273
14. Bell SP, Dutta A (2002) DNA replication in eukaryotic cells. Annu Rev Biochem 71:333-374
15. Belotserkovskaya R, Oh S, Bondarenko VA, Orphanides G, Studitsky VM, Reinberg D (2003) FACT facilitates transcription-dependent nucleosome alteration. Science 301:1090-1093
16. Belotserkovskaya R, Saunders A, Lis JT, Reinberg D (2004) Transcription through chromatin: Understanding a complex FACT. Biochim Biophys Acta 1677:87-99
17. Biswas D, Yu Y, Prall M, Formosa T, Stillman DJ (2005) The yeast FACT complex has a role in transcriptional initiation. Mol Cell Biol 25:5812-5822
18. Bochar DA, Savard J, Wang W, Lafleur DW, Moore P, Cote J, Shiekhattar R (2000) A family of chromatin remodeling factors related to Williams syndrome transcription factor. Proc Natl Acad Sci USA 97:1038-1043
19. Bozhenok L, Wade PA, Varga-Weisz P (2002) WSTF-ISWI chromatin remodeling complex targets heterochromatic replication foci. Embo J 21:2231-2241
20. Brewster NK, Johnston GC, Singer RA (1998) Characterization of the CP complex, an abundant dimer of Cdc68 and Pob3 proteins that regulates yeast transcriptional activation and chromatin repression. J Biol Chem 273:21972-21979
21. Chai B, Huang J, Cairns BR, Laurent BC (2005) Distinct roles for the RSC and Swi/Snf ATP-dependent chromatin remodelers in DNA double-strand break repair. Genes Dev 19:1656-1661
22. Citterio E, Van Den Boom V, Schnitzler G, Kanaar R, Bonte E, Kingston RE, Hoeijmakers JH, Vermeulen W (2000) ATP-dependent chromatin remodeling by the Cockayne syndrome B DNA repair-transcription-coupling factor. Mol Cell Biol 20:7643-7653
23. Collins N, Poot RA, Kukimoto I, Garcia-Jimenez C, Dellaire G, Varga-Weisz PD (2002) An ACF1-ISWI chromatin-remodeling complex is required for DNA replication through heterochromatin. Nat Genet 32:627-632
24. Cosgrove MS, Wolberger C (2005) How does the histone code work? Biochem Cell Biol 83:468-476
25. Cvetic C, Walter JC (2005) Eukaryotic origins of DNA replication: Could you please be more specific? Semin Cell Dev Biol 16:343-353
26. Dirscherl SS, Krebs JE (2004) Functional diversity of ISWI complexes. Biochem Cell Biol 82:482-489
27. Donaldson AD (2005) Shaping time: Chromatin structure and the DNA replication programme. Trends Genet 21:444-449
28. Eberharter A, Becker PB (2004) ATP-dependent nucleosome remodelling: factors and functions. J Cell Sci 117:3707-3711
29. Ehrenhofer-Murray AE (2004) Chromatin dynamics at DNA replication, transcription and repair. Eur J Biochem 271:2335-2349
30. Eisen JA, Sweder KS, Hanawalt PC (1995) Evolution of the SNF2 family of proteins: Subfamilies with distinct sequences and functions. Nucleic Acids Res 23:2715-2723
31. Flanagan JF, Peterson CL (1999) A role for the yeast SWI/SNF complex in DNA replication. Nucleic Acids Res 27:2022-2028
32. Formosa T, Eriksson P, Wittmeyer J, Ginn J, Yu Y, Stillman DJ (2001) Spt16-Pob3 and the HMG protein Nhp6 combine to form the nucleosome-binding factor SPN. Embo J 20:3506-3517
33. Fritsch O, Benvenuto G, Bowler C, Molinier J, Hohn B (2004) The INO80 protein controls homologous recombination in Arabidopsis thaliana. Mol Cell 16:479-485
34. Fyodorov DV, Blower MD, Karpen GH, Kadonaga JT (2004) Acf1 confers unique activities to ACF/CHRAC and promotes the formation rather than disruption of chromatin in vivo. Genes Dev 18:170-183
35. Goldmark JP, Fazzio TG, Estep PW, Church GM, Tsukiyama T (2000) The Isw2 chromatin remodeling complex represses early meiotic genes upon recruitment by Ume6p. Cell 103:423-433
36. Guschin D, Geiman TM, Kikyo N, Tremethick DJ, Wolffe AP, Wade PA (2000) Multiple ISWI ATPase complexes from Xenopus laevis. Functional conservation of an ACF/CHRAC homolog. J Biol Chem 275:35248-35255
37. Hakimi MA, Bochar DA, Schmiesing JA, Dong Y, Barak OG, Speicher DW, Yokomori K, Shiekhattar R (2002) A chromatin remodelling complex that loads cohesin onto human chromosomes. Nature 418:994-998
38. Hasan S, Stucki M, Hassa PO, Imhof R, Gehrig P, Hunziker P, Hubscher U, Hottiger MO (2001) Regulation of human flap endonuclease-1 activity by acetylation through the transcriptional coactivator p300. Mol Cell 7:1221-1231
39. Henikoff S, Ahmad K (2005) Assembly of Variant Histones into Chromatin. Annu Rev Cell Dev Biol 21:133-153
40. Huang J, Hsu JM, Laurent BC (2004) The RSC nucleosome-remodeling complex is required for Cohesin's association with chromosome arms. Mol Cell 13:739-750
41. Huang Y (2002) Transcriptional silencing in Saccharomyces cerevisiae and Schizosaccharomyces pombe. Nucleic Acids Res 30:1465-1482
42. Iida T, Araki H (2004) Noncompetitive counteractions of DNA polymerase epsilon and ISW2/yCHRAC for epigenetic inheritance of telomere position effect in Saccharomyces cerevisiae. Mol Cell Biol 24:217-227
43. Ito T, Bulger M, Pazin MJ, Kobayashi R, Kadonaga JT (1997) ACF, an ISWI-containing and ATP-utilizing chromatin assembly and remodeling factor. Cell 90:145-155
44. Jaskelioff M, Van Komen S, Krebs JE, Sung P, Peterson CL (2003) Rad54p is a chromatin remodeling enzyme required for heteroduplex DNA joint formation with chromatin. J Biol Chem 278:9212-9218
45. Kornberg RD, Lorch Y (1999) Twenty-five years of the nucleosome, fundamental particle of the eukaryote chromosome. Cell 98:285-294
46. Krogan NJ, Keogh MC, Datta N, Sawa C, Ryan OW, Ding H, Haw RA, Pootoolal J, Tong A, Canadien V, Richards DP, Wu X, Emili A, Hughes TR, Buratowski S, Greenblatt JF (2003) A Snf2 family ATPase complex required for recruitment of the histone H2A variant Htz1. Mol Cell 12:1565-1576
47. Krogh BO, Symington LS (2004) Recombination proteins in yeast. Annu Rev Genet 38:233-271
48. Kusch T, Florens L, Macdonald WH, Swanson SK, Glaser RL, Yates JR III, Abmayr SM, Washburn MP, Workman JL (2004) Acetylation by Tip60 is required for selective histone variant exchange at DNA lesions. Science 306:2084-2087
49. Kuzminov A (2001) DNA replication meets genetic exchange: Chromosomal damage and its repair by homologous recombination. Proc Natl Acad Sci USA 98:8461-8468
50. Langst G, Becker PB (2001) Nucleosome mobilization and positioning by ISWI-containing chromatin-remodeling factors. J Cell Sci 114:2561-2568
51. Lazzaro MA, Picketts DJ (2001) Cloning and characterization of the murine Imitation Switch (ISWI) genes: Differential expression patterns suggest distinct developmental roles for Snf2h and Snf2l. J Neurochem 77:1145-1156
52. LeRoy G, Loyola A, Lane WS, Reinberg D (2000) Purification and characterization of a human factor that assembles and remodels chromatin. J Biol Chem 275:14787-14790
53. LeRoy G, Orphanides G, Lane WS, Reinberg D (1998) Requirement of RSF and FACT for transcription of chromatin templates in vitro. Science 282:1900-1904
54. Loyola A, Almouzni G (2004) Histone chaperones, a supporting role in the limelight. Biochim Biophys Acta 1677:3-11
55. Luger K, Hansen JC (2005) Nucleosome and chromatin fiber dynamics. Curr Opin Struct Biol 15:188-196
56. Lusser A, Kadonaga JT (2003) Chromatin remodeling by ATP-dependent molecular machines. Bioessays 25:1192-1200
57. MacCallum DE, Losada A, Kobayashi R, Hirano T (2002) ISWI remodeling complexes in Xenopus egg extracts: Identification as major chromosomal components that are regulated by INCENP-aurora B. Mol Biol Cell 13:25-39
58. Maga G, Hubscher U (2003) Proliferating cell nuclear antigen (PCNA): A dancer with many partners. J Cell Sci 116:3051-3060
59. McConnell AD, Gelbart ME, Tsukiyama T (2004) Histone fold protein Dls1p is required for Isw2-dependent chromatin remodeling in vivo. Mol Cell Biol 24:2605-2613
60. McNairn AJ, Gilbert DM (2003) Epigenomic replication: Linking epigenetics to DNA replication. Bioessays 25:647-656
61. Meijsing SH, Ehrenhofer-Murray AE (2001) The silencing complex SAS-I links histone acetylation to the assembly of repressed chromatin by CAF-I and Asf1 in Saccharomyces cerevisiae. Genes Dev 15:3169-3182
62. Milutinovic S, Zhuang Q, Szyf M (2002) Proliferating cell nuclear antigen associates with histone deacetylase activity, integrating DNA replication and chromatin modification. J Biol Chem 277:20974-20978
63. Mizuguchi G, Shen X, Landry J, Wu WH, Sen S, Wu C (2004) ATP-driven exchange of histone H2AZ variant catalyzed by SWR1 chromatin remodeling complex. Science 303:343-348
64. Moore JD, Krebs JE (2004) Histone modifications and DNA double-strand break repair. Biochem Cell Biol 82:446-452
65. Morrison AJ, Highland J, Krogan NJ, Arbel-Eden A, Greenblatt JF, Haber JE, Shen X (2004) INO80 and gamma-H2AX interaction links ATP-dependent chromatin remodeling to DNA damage repair. Cell 119:767-775
66. Morrison AJ, Shen X (2005) DNA repair in the context of chromatin. Cell Cycle 4:568-571
67. O'Donnell AF, Brewster NK, Kurniawan J, Minard LV, Johnston GC, Singer RA (2004) Domain organization of the yeast histone chaperone FACT: The conserved N-terminal domain of FACT subunit Spt16 mediates recovery from replication stress. Nucleic Acids Res 32:5894-5906
68. Okuhara K, Ohta K, Seo H, Shioda M, Yamada T, Tanaka Y, Dohmae N, Seyama Y, Shibata T, Murofushi H (1999) A DNA unwinding factor involved in DNA replication in cell-free extracts of Xenopus eggs. Curr Biol 9:341-350
69. Orphanides G, LeRoy G, Chang CH, Luse DS, Reinberg D (1998) FACT, a factor that facilitates transcript elongation through nucleosomes. Cell 92:105-116
70. Orphanides G, Wu WH, LaneWS, Hampsey M, Reinberg D (1999) The chromatin-specific transcription elongation factor FACT comprises human SPT16 and SSRP1 proteins. Nature 400:284-288
71. Osada S, Sutton A, Muster N, Brown CE, Yates JR 3rd, Sternglanz R, Workman JL (2001) The yeast SAS (something about silencing) protein complex contains a MYST-type putative acetyltransferase and functions with chromatin assembly factor ASF1. Genes Dev 15:3155-3168
72. Peterson CL, Laniel MA (2004) Histones and histone modifications. Curr Biol 14:R546-R551
73. Poot RA, Bozhenok L, van den Berg DL, Hawkes N, Varga-Weisz PD (2005) Chromatin remodeling by WSTF-ISWI at the replication site: Opening a window of opportunity for epigenetic inheritance? Cell Cycle 4:543-546
74. Poot RA, Bozhenok L, van den Berg DL, Steffensen S, Ferreira F, Grimaldi M, Gilbert N, Ferreira J, Varga-Weisz PD (2004) The Williams syndrome transcription factor interacts with PCNA to target chromatin remodelling by ISWI to replication foci. Nat Cell Biol 6:1236-1244
75. Poot RA, Dellaire G, Hulsmann BB, Grimaldi MA, Corona DF, Becker PB, Bickmore WA, Varga-Weisz PD (2000) HuCHRAC, a human ISWI chromatin remodelling complex contains hACF1 and two novel histone-fold proteins. Embo J 19:3377-3387
76. Rhoades AR, Ruone S, Formosa T (2004) Structural features of nucleosomes reorganized by yeast FACT and its HMG box component, Nhp6. Mol Cell Biol 24:3907-3917
77. Riedel CG, Gregan J, Gruber S, Nasmyth K (2004) Is chromatin remodeling required to build sister-chromatid cohesion? Trends Biochem Sci 29:389-392
78. Santoro R, Grummt I (2005) Epigenetic mechanism of rRNA gene silencing: temporal order of NoRC-mediated histone modification, chromatin remodeling, and DNA methylation. Mol Cell Biol 25:2539-2546
79. Schalch T, Duda S, Sargent DF, Richmond TJ (2005) X-ray structure of a tetranucleosome and its implications for the chromatin fibre. Nature 436:138-141
80. Schlesinger MB, Formosa T (2000) POB3 is required for both transcription and replication in the yeast Saccharomyces cerevisiae. Genetics 155:1593-1606
81. Seo H, Okuhara K, Kurumizaka H, Yamada T, Shibata T, Ohta K, Akiyama T, Murofushi H (2003) Incorporation of DUF/FACT into chromatin enhances the accessibility of nucleosomal DNA. Biochem Biophys Res Commun 303:8-13
82. Smirnova M, Van Komen S, Sung P, Klein HL (2004) Effects of tumor-associated mutations on Rad54 functions. J Biol Chem 279:24081-24088
83. Stopka T, Skoultchi AI (2003) The ISWI ATPase Snf2h is required for early mouse development. Proc Natl Acad Sci USA 100:14097-14102
84. Strohner R, Nemeth A, Jansa P, Hofmann-Rohrer U, Santoro R, Langst G, Grummt I (2001) NoRC - a novel member of mammalian ISWI-containing chromatin remodeling machines. Embo J 20:4892-4900
85. Suter B, Tong A, Chang M, Yu L, Brown GW, Boone C, Rine J (2004) The origin recognition complex links replication, sister chromatid cohesion and transcriptional silencing in Saccharomyces cerevisiae. Genetics 167:579-591
86. Tackett AJ, Dilworth DJ, Davey MJ, O'Donnell M, Aitchison JD, Rout MP, Chait BT (2005) Proteomic and genomic characterization of chromatin complexes at a boundary. J Cell Biol 169:35-47
87. Taddei A, Maison C, Roche D, Almouzni G (2001) Reversible disruption of pericentric heterochromatin and centromere function by inhibiting deacetylases. Nat Cell Biol 3:114-120
88. Taddei A, Roche D, Sibarita JB, Turner BM, Almouzni G (1999) Duplication and maintenance of heterochromatin domains. J Cell Biol 147:1153-1166
89. Tan BC, Lee SC (2004) Nek9, a novel FACT-associated protein, modulates interphase progression. J Biol Chem 279:9321-9330
90. Tan TL, Kanaar R, Wyman C (2003) Rad54, a Jack of all trades in homologous recombination. DNA Repair (Amst) 2:787-794
91. Tsukiyama T, Palmer J, Landel CC, Shiloach J, Wu C (1999) Characterization of the imitation switch subfamily of ATP-dependent chromatin-remodeling factors in Saccharomyces cerevisiae. Genes Dev 13:686-697
92. Tsukiyama T, Wu C (1995) Purification and properties of an ATP-dependent nucleosome remodeling factor. Cell 83:1011-1020
93. van Attikum H, Fritsch O, Hohn B, Gasser SM (2004) Recruitment of the INO80 complex by H2A phosphorylation links ATP-dependent chromatin remodeling with DNA double-strand break repair. Cell 119:777-788
94. van Attikum H, Gasser SM (2005) ATP-dependent chromatin remodeling and dna doublestrand break repair. Cell Cycle 4:1011-1014
95. Varga-Weisz PD, Wilm M, Bonte E, Dumas K, Mann M, Becker PB (1997) Chromatin-remodelling factor CHRAC contains the ATPases ISWI and topoisomerase II. Nature 388:598-602
96. Vary JC Jr, Gangaraju VK, Qin J, Landel CC, Kooperberg C, Bartholomew B, Tsukiyama T (2003) Yeast Isw1p forms two separable complexes in vivo. Mol Cell Biol 23:80-91
97. Vogelauer M, Rubbi L, Lucas I, Brewer BJ, Grunstein M (2002) Histone acetylation regulates the time of replication origin firing. Mol Cell 10:1223-1233
98. Walfridsson J, Bjerling P, Thalen M, Yoo EJ, Park SD, Ekwall K (2005) The CHD remodeling factor Hrp1 stimulates CENP-A loading to centromeres. Nucleic Acids Res 33:2868-2879
99. Wiren M, Silverstein RA, Sinha I, Walfridsson J, Lee HM, Laurenson P, Pillus L, Robyr D, Grunstein M, Ekwall K (2005) Genomewide analysis of nucleosome density histone acetylation and HDAC function in fission yeast. Embo J 24:2906-2918
100. Wittmeyer J, Joss L, Formosa T (1999) Spt16 and Pob3 of Saccharomyces cerevisiae form an essential, abundant heterodimer that is nuclear, chromatin-associated, and copurifies with DNA polymerase alpha. Biochemistry 38:8961-8971
101. Wu R, Terry AV, Singh PB, Gilbert DM (2005) Differential subnuclear localization and replication timing of histone H3 lysine 9 methylation states. Mol Biol Cell 16:2872-2881
102. Yamada T, Fischle W, Sugiyama T, Allis CD, Grewal SI (2005) The nucleation and maintenance of heterochromatin by a histone deacetylase in fission yeast. Mol Cell 20:173-185
103. Yamada T, Okuhara K, Iwamatsu A, Seo H, Ohta K, Shibata T, Murofushi H (2000) p97 ATPase, an ATPase involved in membrane fusion, interacts with DNA unwinding factor (DUF) that functions in DNA replication. FEBS Lett 466:287-291
104. Yasui D, Miyano M, Cai S, Varga-Weisz P, Kohwi-Shigematsu T (2002) SATB1 targets chromatin remodelling to regulate genes over long distances. Nature 419:641-645
105. Zhou J, Chau CM, Deng Z, Shiekhattar R, Spindler MP, Schepers A, Lieberman PM (2005) Cell cycle regulation of chromatin at an origin of DNA replication. Embo J 24:1406-1417
106. Zhou Y, Wang TS (2004) A coordinated temporal interplay of nucleosome reorganization factor, sister chromatin cohesion factor, and DNA polymerase alpha facilitates DNA replication. Mol Cell Biol 24:9568-9579