Mechanisms of ATP dependent chromatin remodeling

Mutation Research - Fundamental and Molecular Mechanisms of Mutagenesis

Volumn 618, Issue 1-2, 2007, Pages 3-17

  Gangaraju, Vamsi K ^a   Bartholomew, Blaine ^a  

^a SOUTHERN ILLINOIS UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Bulge propagation; CHD; Chromatin remodeling; INO80; ISWI; Nucleosome; Nucleosome spacing; SWI SNF; SWR1; Twist diffusion

Indexed keywords

ADENOSINE TRIPHOSPHATE; DNA BINDING PROTEIN; HISTONE;

ARTICLE; BINDING AFFINITY; CHROMATIN ASSEMBLY AND DISASSEMBLY; CHROMATIN STRUCTURE; DNA REPAIR; DROSOPHILA; ENZYME ACTIVE SITE; GENE SWITCHING; NUCLEOSOME; PRIORITY JOURNAL;

ADENOSINE TRIPHOSPHATE; ANIMALS; CATALYTIC DOMAIN; CHROMATIN; CHROMATIN ASSEMBLY AND DISASSEMBLY; DIFFUSION; HISTONES; HUMANS; NUCLEOSOMES; PROTEIN BINDING; PROTEIN STRUCTURE, TERTIARY; SACCHAROMYCES CEREVISIAE;

EID: 34147102171     PISSN: 00275107     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.mrfmmm.2006.08.015     Document Type: Article

References (152)

1. Kornberg R.D., and Lorch Y. Twenty-five years of the nucleosome, fundamental particle of the eukaryote chromosome. Cell 98 (1999) 285-294
2. Strahl B.D., and Allis C.D. The language of covalent histone modifications. Nature 403 (2000) 41-45
3. Becker P.B., and Horz W. ATP-dependent nucleosome remodeling. Annu. Rev. Biochem. 71 (2002) 247-273
4. Luger K., Mader A.W., Richmond R.K., Sargent D.F., and Richmond T.J. Crystal structure of the nucleosome core particle at 2.8 Å resolution. Nature 389 (1997) 251-260
5. Peterson C.L., and Herskowitz I. Characterization of the yeast SWI1, SWI2, and SWI3 genes, which encode a global activator of transcription. Cell 68 (1992) 573-583
6. Sudarsanam P., and Winston F. The Swi/Snf family nucleosome-remodeling complexes and transcriptional control. Trends Genet. 16 (2000) 345-351
7. Workman J.L., and Kingston R.E. Alteration of nucleosome structure as a mechanism of transcriptional regulation. Annu. Rev. Biochem. 67 (1998) 545-579
8. Du J., Nasir I., Benton B.K., Kladde M.P., and Laurent B.C. Sth1p, a Saccharomyces cerevisiae Snf2p/Swi2p homolog, is an essential ATPase in RSC and differs from Snf/Swi in its interactions with histones and chromatin-associated proteins. Genetics 150 (1998) 987-1005
9. Cairns B.R., Schlichter A., Erdjument-Bromage H., Tempst P., Kornberg R.D., and Winston F. Two functionally distinct forms of the RSC nucleosome-remodeling complex, containing essential AT hook, BAH, and bromodomains. Mol. Cell 4 (1999) 715-723
10. Mohrmann L., and Verrijzer C.P. Composition and functional specificity of SWI2/SNF2 class chromatin remodeling complexes. Biochim. Biophys. Acta 1681 (2005) 59-73
11. Wang W. The SWI/SNF family of ATP-dependent chromatin remodelers: similar mechanisms for diverse functions. Curr. Top. Microbiol. Immunol. 274 (2003) 143-169
12. Bochar D.A., Wang L., Beniya H., Kinev A., Xue Y., Lane W.S., Wang W., Kashanchi F., and Shiekhattar R. BRCA1 is associated with a human SWI/SNF-related complex: linking chromatin remodeling to breast cancer. Cell 102 (2000) 257-265
13. Decristofaro M.F., Betz B.L., Rorie C.J., Reisman D.N., Wang W., and Weissman B.E. Characterization of SWI/SNF protein expression in human breast cancer cell lines and other malignancies. J. Cell Physiol. 186 (2001) 136-145
14. Sif S., Saurin A.J., Imbalzano A.N., and Kingston R.E. Purification and characterization of mSin3A-containing Brg1 and hBrm chromatin remodeling complexes. Genes Dev. 15 (2001) 603-618
15. Pal S., Yun R., Datta A., Lacomis L., Erdjument-Bromage H., Kumar J., Tempst P., and Sif S. mSin3A/histone deacetylase 2- and PRMT5-containing Brg1 complex is involved in transcriptional repression of the Myc target gene cad. Mol. Cell. Biol. 23 (2003) 7475-7487
16. Pal S., Vishwanath S.N., Erdjument-Bromage H., Tempst P., and Sif S. Human SWI/SNF-associated PRMT5 methylates histone H3 arginine 8 and negatively regulates expression of ST7 and NM23 tumor suppressor genes. Mol. Cell. Biol. 24 (2004) 9630-9645
17. Lee K.K., Prochasson P., Florens L., Swanson S.K., Washburn M.P., and Workman J.L. Proteomic analysis of chromatin-modifying complexes in Saccharomyces cerevisiae identifies novel subunits. Biochem. Soc. Trans. 32 (2004) 899-903
18. Graumann J., Dunipace L.A., Seol J.H., McDonald W.H., Yates III J.R., Wold B.J., and Deshaies R.J. Applicability of tandem affinity purification MudPIT to pathway proteomics in yeast. Mol. Cell. Proteomics 3 (2004) 226-237
19. de la Serna I.L., Ohkawa Y., Berkes C.A., Bergstrom D.A., Dacwag C.S., Tapscott S.J., and Imbalzano A.N. MyoD targets chromatin remodeling complexes to the myogenin locus prior to forming a stable DNA-bound complex. Mol. Cell. Biol. 25 (2005) 3997-4009
20. de la Serna I.L., Carlson K.A., and Imbalzano A.N. Mammalian SWI/SNF complexes promote MyoD-mediated muscle differentiation. Nat. Genet. 27 (2001) 187-190
21. Ohkawa Y., Marfella C.G., and Imbalzano A.N. Skeletal muscle specification by myogenin and Mef2D via the SWI/SNF ATPase Brg1. EMBO J. 25 (2006) 490-501
22. Simone C., Forcales S.V., Hill D.A., Imbalzano A.N., Latella L., and Puri P.L. p38 pathway targets SWI-SNF chromatin-remodeling complex to muscle-specific loci. Nat. Genet. 36 (2004) 738-743
23. Lickert H., Takeuchi J.K., Von Both I., Walls J.R., McAuliffe F., Adamson S.L., Henkelman R.M., Wrana J.L., Rossant J., and Bruneau B.G. Baf60c is essential for function of BAF chromatin remodelling complexes in heart development. Nature 432 (2004) 107-112
24. Vradii D., Wagner S., Doan D.N., Nickerson J.A., Montecino M., Lian J.B., Stein J.L., van Wijnen A.J., Imbalzano A.N., and Stein G.S. Brg1, the ATPase subunit of the SWI/SNF chromatin remodeling complex, is required for myeloid differentiation to granulocytes. J. Cell Physiol. 206 (2006) 112-118
25. Young D.W., Pratap J., Javed A., Weiner B., Ohkawa Y., van Wijnen A., Montecino M., Stein G.S., Stein J.L., Imbalzano A.N., and Lian J.B. SWI/SNF chromatin remodeling complex is obligatory for BMP2-induced, Runx2-dependent skeletal gene expression that controls osteoblast differentiation. J. Cell. Biochem. 94 (2005) 720-730
26. Seo S., Herr A., Lim J.W., Richardson G.A., Richardson H., and Kroll K.L. Geminin regulates neuronal differentiation by antagonizing Brg1 activity. Genes Dev. 19 (2005) 1723-1734
27. Matsumoto S., Banine F., Struve J., Xing R., Adams C., Liu Y., Metzger D., Chambon P., Rao M.S., and Sherman L.S. Brg1 is required for murine neural stem cell maintenance and gliogenesis. Dev. Biol. 289 (2006) 372-383
28. Olave I., Wang W., Xue Y., Kuo A., and Crabtree G.R. Identification of a polymorphic, neuron-specific chromatin remodeling complex. Genes Dev. 16 (2002) 2509-2517
29. Battaglioli E., Andres M.E., Rose D.W., Chenoweth J.G., Rosenfeld M.G., Anderson M.E., and Mandel G. REST repression of neuronal genes requires components of the hSWI.SNF complex. J. Biol. Chem. 277 (2002) 41038-41045
30. Salma N., Xiao H., Mueller E., and Imbalzano A.N. Temporal recruitment of transcription factors and SWI/SNF chromatin-remodeling enzymes during adipogenic induction of the peroxisome proliferator-activated receptor gamma nuclear hormone receptor. Mol. Cell. Biol. 24 (2004) 4651-4663
31. Inayoshi Y., Miyake K., Machida Y., Kaneoka H., Terajima M., Dohda T., Takahashi M., and Iijima S. Mammalian chromatin remodeling complex SWI/SNF is essential for enhanced expression of the albumin gene during liver development. J. Biochem. (Tokyo) 139 (2006) 177-188
32. Mudhasani R., and Fontes J.D. Multiple interactions between BRG1 and MHC class II promoter binding proteins. Mol. Immunol. 42 (2005) 673-682
33. Gebuhr T.C., Kovalev G.I., Bultman S., Godfrey V., Su L., and Magnuson T. The role of Brg1, a catalytic subunit of mammalian chromatin-remodeling complexes, in T cell development. J. Exp. Med. 198 (2003) 1937-1949
34. Chai B., Huang J., Cairns B.R., and Laurent B.C. Distinct roles for the RSC and Swi/Snf ATP-dependent chromatin remodelers in DNA double-strand break repair. Genes Dev. 19 (2005) 1656-1661
35. Huang J., Liang B., Qiu J., and Laurent B.C. ATP-dependent chromatin-remodeling complexes in DNA double-strand break repair: remodeling, pairing and (re)pairing. Cell Cycle 4 (2005) 1713-1715
36. Huang J., and Laurent B.C. A Role for the RSC chromatin remodeler in regulating cohesion of sister chromatid arms. Cell Cycle 3 (2004) 973-975
37. Huang J., Hsu J.M., and Laurent B.C. The RSC nucleosome-remodeling complex is required for Cohesin's association with chromosome arms. Mol. Cell 13 (2004) 739-750
38. Chang C.R., Wu C.S., Hom Y., and Gartenberg M.R. Targeting of cohesin by transcriptionally silent chromatin. Genes Dev. 19 (2005) 3031-3042
39. Batsche E., Yaniv M., and Muchardt C. The human SWI/SNF subunit Brm is a regulator of alternative splicing. Nat. Struct. Mol. Biol. 13 (2006) 22-29
40. Dror V., and Winston F. The Swi/Snf chromatin remodeling complex is required for ribosomal DNA and telomeric silencing in Saccharomyces cerevisiae. Mol. Cell. Biol. 24 (2004) 8227-8235
41. Thoma N.H., Czyzewski B.K., Alexeev A.A., Mazin A.V., Kowalczykowski S.C., and Pavletich N.P. Structure of the SWI2/SNF2 chromatin-remodeling domain of eukaryotic Rad54. Nat. Struct. Mol. Biol. 12 (2005) 350-356
42. Durr H., Korner C., Muller M., Hickmann V., and Hopfner K.P. X-ray structures of the Sulfolobus solfataricus SWI2/SNF2 ATPase core and its complex with DNA. Cell 121 (2005) 363-373
43. Dhalluin C., Carlson J.E., Zeng L., He C., Aggarwal A.K., and Zhou M.M. Structure and ligand of a histone acetyltransferase bromodomain. Nature 399 (1999) 491-496
44. Hudson B.P., Martinez-Yamout M.A., Dyson H.J., and Wright P.E. Solution structure and acetyl-lysine binding activity of the GCN5 bromodomain. J. Mol. Biol. 304 (2000) 355-370
45. Jacobson R.H., Ladurner A.G., King D.S., and Tjian R. Structure and function of a human TAFII250 double bromodomain module. Science 288 (2000) 1422-1425
46. Marmorstein R., and Berger S.L. Structure and function of bromodomains in chromatin-regulating complexes. Gene 272 (2001) 1-9
47. Owen D.J., Ornaghi P., Yang J.C., Lowe N., Evans P.R., Ballario P., Neuhaus D., Filetici P., and Travers A.A. The structural basis for the recognition of acetylated histone H4 by the bromodomain of histone acetyltransferase gcn5p. EMBO J. 19 (2000) 6141-6149
48. Zeng L., and Zhou M.M. Bromodomain: an acetyl-lysine binding domain. FEBS Lett. 513 (2002) 124-128
49. Hassan A.H., Prochasson P., Neely K.E., Galasinski S.C., Chandy M., Carrozza M.J., and Workman J.L. Function and selectivity of bromodomains in anchoring chromatin-modifying complexes to promoter nucleosomes. Cell 111 (2002) 369-379
50. Ladurner A.G., Inouye C., Jain R., and Tjian R. Bromodomains mediate an acetyl-histone encoded antisilencing function at heterochromatin boundaries. Mol. Cell 11 (2003) 365-376
51. Collins R.T., Furukawa T., Tanese N., and Treisman J.E. Osa associates with the Brahma chromatin remodeling complex and promotes the activation of some target genes. EMBO J. 18 (1999) 7029-7040
52. Patsialou A., Wilsker D., and Moran E. DNA-binding properties of ARID family proteins. Nucleic Acids Res. 33 (2005) 66-80
53. Wilsker D., Patsialou A., Dallas P.B., and Moran E. ARID proteins: a diverse family of DNA binding proteins implicated in the control of cell growth, differentiation, and development. Cell Growth Differ. 13 (2002) 95-106
54. Herrscher R.F., Kaplan M.H., Lelsz D.L., Das C., Scheuermann R., and Tucker P.W. The immunoglobulin heavy-chain matrix-associating regions are bound by Bright: a B cell-specific trans-activator that describes a new DNA-binding protein family. Genes Dev. 9 (1995) 3067-3082
55. Gregory S.L., Kortschak R.D., Kalionis B., and Saint R. Characterization of the dead ringer gene identifies a novel, highly conserved family of sequence-specific DNA-binding proteins. Mol. Cell. Biol. 16 (1996) 792-799
56. Kim S., Zhang Z., Upchurch S., Isern N., and Chen Y. Structure and DNA-binding sites of the SWI1 AT-rich interaction domain (ARID) suggest determinants for sequence-specific DNA recognition. J. Biol. Chem. 279 (2004) 16670-16676
57. Iwahara J., and Clubb R.T. Solution structure of the DNA binding domain from Dead ringer, a sequence-specific AT-rich interaction domain (ARID). EMBO J. 18 (1999) 6084-6094
58. Wilsker D., Patsialou A., Zumbrun S.D., Kim S., Chen Y., Dallas P.B., and Moran E. The DNA-binding properties of the ARID-containing subunits of yeast and mammalian SWI/SNF complexes. Nucleic Acids Res. 32 (2004) 1345-1353
59. Qian C., Zhang Q., Li S., Zeng L., Walsh M.J., and Zhou M.M. Structure and chromosomal DNA binding of the SWIRM domain. Nat. Struct. Mol. Biol. 12 (2005) 1078-1085
60. Aravind L., and Iyer L.M. The SWIRM domain: a conserved module found in chromosomal proteins points to novel chromatin-modifying activities. Genome Biol. 3 (2002) RESEARCH0039
61. Da G., Lenkart J., Zhao K., Shiekhattar R., Cairns B.R., and Marmorstein R. Structure and function of the SWIRM domain, a conserved protein module found in chromatin regulatory complexes. Proc. Natl. Acad. Sci. U.S.A. 103 (2006) 2057-2062
62. Shi Y.J., Matson C., Lan F., Iwase S., Baba T., and Shi Y. Regulation of LSD1 histone demethylase activity by its associated factors. Mol. Cell 19 (2005) 857-864
63. de la Cruz X., Lois S., Sanchez-Molina S., and Martinez-Balbas M.A. Do protein motifs read the histone code?. Bioessays 27 (2005) 164-175
64. Barbaric S., Reinke H., and Horz W. Multiple mechanistically distinct functions of SAGA at the PHO5 promoter. Mol. Cell. Biol. 23 (2003) 3468-3476
65. Boyer L.A., Langer M.R., Crowley K.A., Tan S., Denu J.M., and Peterson C.L. Essential role for the SANT domain in the functioning of multiple chromatin remodeling enzymes. Mol. Cell 10 (2002) 935-942
66. Sterner D.E., Wang X., Bloom M.H., Simon G.M., and Berger S.L. The SANT domain of Ada2 is required for normal acetylation of histones by the yeast SAGA complex. J. Biol. Chem. 277 (2002) 8178-8186
67. You A., Tong J.K., Grozinger C.M., and Schreiber S.L. CoREST is an integral component of the CoREST - human histone deacetylase complex. Proc. Natl. Acad. Sci. U.S.A. 98 (2001) 1454-1458
68. Guenther M.G., Barak O., and Lazar M.A. The SMRT and N-CoR corepressors are activating cofactors for histone deacetylase 3. Mol. Cell. Biol. 21 (2001) 6091-6101
69. Yu J., Li Y., Ishizuka T., Guenther M.G., and Lazar M.A. A SANT motif in the SMRT corepressor interprets the histone code and promotes histone deacetylation. EMBO J. 22 (2003) 3403-3410
70. Boyer L.A., Latek R.R., and Peterson C.L. The SANT domain: a unique histone-tail-binding module?. Nat. Rev. Mol. Cell. Biol. 5 (2004) 158-163
71. Mo X., Kowenz-Leutz E., Laumonnier Y., Xu H., and Leutz A. Histone H3 tail positioning and acetylation by the c-Myb but not the v-Myb DNA-binding SANT domain. Genes Dev. 19 (2005) 2447-2457
72. Grüne T., Brzeski J., Eberharter A., Clapier C.R., Corona D.F.V., Becker P.B., and Müller C.W. Crystal structure and functional analysis of a nucleosome recognition module of the remodeling factor ISWI. Mol. Cell 12 (2003) 449-460
73. Tsukiyama T., and Wu C. Purification and properties of an ATP-dependent nucleosome remodeling factor. Cell 83 (1995) 1011-1020
74. Varga-Weisz P.D., Wilm M., Bonte E., Dumas K., Mann M., and Becker P.B. Chromatin-remodelling factor CHRAC contains the ATPases ISWI and topoisomerase II. Nature 388 (1997) 598-602
75. Tsukiyama T., Palmer J., Landel C.C., Shiloach J., and Wu C. Characterization of the imitation switch subfamily of ATP-dependent chromatin-remodeling factors in Saccharomyces cerevisiae. Genes Dev. 13 (1999) 686-697
76. Strohner R., Nemeth A., Jansa P., Hofmann-Rohrer U., Santoro R., Langst G., and Grummt I. NoRC-a novel member of mammalian ISWI-containing chromatin remodeling machines. EMBO J. 20 (2001) 4892-4900
77. Aalfs J.D., Narlikar G.J., and Kingston R.E. Functional differences between the human ATP-dependent nucleosome remodeling proteins BRG1 and SNF2H. J. Biol. Chem. 276 (2001) 34270-34278
78. Lazzaro M.A., and Picketts D.J. Cloning and characterization of the murine Imitation Switch (ISWI) genes: differential expression patterns suggest distinct developmental roles for Snf2h and Snf2l. J. Neurochem. 77 (2001) 1145-1156
79. Guschin D., Geiman T.M., Kikyo N., Tremethick D.J., Wolffe A.P., and Wade P.A. Multiple ISWI ATPase complexes from xenopus laevis. Functional conservation of an ACF/CHRAC homolog. J. Biol. Chem. 275 (2000) 35248-35255
80. Grune T., Brzeski J., Eberharter A., Clapier C.R., Corona D.F., Becker P.B., and Muller C.W. Crystal structure and functional analysis of a nucleosome recognition module of the remodeling factor ISWI. Mol. Cell 12 (2003) 449-460
81. Aasland R., Stewart A.F., and Gibson T. The SANT domain: a putative DNA-binding domain in the SWI-SNF and ADA complexes, the transcriptional co-repressor N-CoR and TFIIIB. Trends Biochem. Sci. 21 (1996) 87-88
82. Langst G., Bonte E.J., Corona D.F., and Becker P.B. Nucleosome movement by CHRAC and ISWI without disruption or trans-displacement of the histone octamer. Cell 97 (1999) 843-852
83. Tsukiyama T., Daniel C., Tamkun J., and Wu C. ISWI, a member of the SWI2/SNF2 ATPase family, encodes the 140 kDa subunit of the nucleosome remodeling factor. Cell 83 (1995) 1021-1026
84. Okada M., and Hirose S. Chromatin remodeling mediated by Drosophila GAGA factor and ISWI activates fushi tarazu gene transcription in vitro. Mol. Cell. Biol. 18 (1998) 2455-2461
85. Georgel P.T., Tsukiyama T., and Wu C. Role of histone tails in nucleosome remodeling by Drosophila NURF. EMBO J. 16 (1997) 4717-4726
86. Hamiche A., Kang J.G., Dennis C., Xiao H., and Wu C. Histone tails modulate nucleosome mobility and regulate ATP-dependent nucleosome sliding by NURF. Proc. Natl. Acad. Sci. U.S.A. 98 (2001) 14316-14321
87. Mizuguchi G., Tsukiyama T., Wisniewski J., and Wu C. Role of nucleosome remodeling factor NURF in transcriptional activation of chromatin. Mol. Cell 1 (1997) 141-150
88. Badenhorst P., Voas M., Rebay I., and Wu C. Biological functions of the ISWI chromatin remodeling complex NURF. Genes Dev. 16 (2002) 3186-3198
89. Badenhorst P., Xiao H., Cherbas L., Kwon S.Y., Voas M., Rebay I., Cherbas P., and Wu C. The Drosophila nucleosome remodeling factor NURF is required for Ecdysteroid signaling and metamorphosis. Genes Dev. 19 (2005) 2540-2545
90. Hamiche A., Sandaltzopoulos R., Gdula D.A., and Wu C. ATP-dependent histone octamer sliding mediated by the chromatin remodeling complex NURF. Cell 97 (1999) 833-842
91. Xiao H., Sandaltzopoulos R., Wang H.M., Hamiche A., Ranallo R., Lee K.M., Fu D., and Wu C. Dual functions of largest NURF subunit NURF301 in nucleosome sliding and transcription factor interactions. Mol. Cell 8 (2001) 531-543
92. Kang J.G., Hamiche A., and Wu C. GAL4 directs nucleosome sliding induced by NURF. EMBO J. 21 (2002) 1406-1413
93. Ito T., Bulger M., Pazin M.J., Kobayashi R., and Kadonaga J.T. ACF, an ISWI-containing and ATP-utilizing chromatin assembly and remodeling factor. Cell 90 (1997) 145-155
94. Fyodorov D.V., and Kadonaga J.T. Dynamics of ATP-dependent chromatin assembly by ACF. Nature 418 (2002) 897-900
95. Bonaldi T., Langst G., Strohner R., Becker P.B., and Bianchi M.E. The DNA chaperone HMGB1 facilitates ACF/CHRAC-dependent nucleosome sliding. EMBO J. 21 (2002) 6865-6873
96. Fyodorov D.V., Blower M.D., Karpen G.H., and Kadonaga J.T. Acf1 confers unique activities to ACF/CHRAC and promotes the formation rather than disruption of chromatin in vivo. Genes Dev. 18 (2004) 170-183
97. Corona D.F., Eberharter A., Budde A., Deuring R., Ferrari S., Varga-Weisz P., Wilm M., Tamkun J., and Becker P.B. Two histone fold proteins, CHRAC-14 and CHRAC-16, are developmentally regulated subunits of chromatin accessibility complex (CHRAC). EMBO J. 19 (2000) 3049-3059
98. Mellor J., and Morillon A. ISWI complexes in Saccharomyces cerevisiae. Biochim. Biophys. Acta 1677 (2004) 100-112
99. Vary Jr. J.C., Gangaraju V.K., Qin J., Landel C.C., Kooperberg C., Bartholomew B., and Tsukiyama T. Yeast Isw1p forms two separable complexes in vivo. Mol. Cell. Biol. 23 (2003) 80-91
100. Gelbart M.E., Rechsteiner T., Richmond T.J., and Tsukiyama T. Interactions of Isw2 chromatin remodeling complex with nucleosomal arrays: analyses using recombinant yeast histones and immobilized templates. Mol. Cell. Biol. 21 (2001) 2098-2106
101. Ito T., Levenstein M.E., Fyodorov D.V., Kutach A.K., Kobayashi R., and Kadonaga J.T. ACF consists of two subunits, Acf1 and ISWI, that function cooperatively in the ATP-dependent catalysis of chromatin assembly. Genes Dev. 13 (1999) 1529-1539
102. Eberharter A., Vetter I., Ferreira R., and Becker P.B. ACF1 improves the effectiveness of nucleosome mobilization by ISWI through PHD-histone contacts. EMBO J. 23 (2004) 4029-4039
103. Tsukiyama T., and Wu C. Chromatin remodeling and transcription. Curr. Opin. Genet. Dev. 7 (1997) 182-191
104. Delmas V., Stokes D.G., and Perry R.P. A mammalian DNA-binding protein that contains a chromodomain and an SNF2/SWI2-like helicase domain. Proc. Natl. Acad. Sci. U.S.A. 90 (1993) 2414-2418
105. Stokes D.G., and Perry R.P. DNA-binding and chromatin localization properties of CHD1. Mol. Cell. Biol. 15 (1995) 2745-2753
106. Stokes D.G., Tartof K.D., and Perry R.P. CHD1 is concentrated in interbands and puffed regions of Drosophila polytene chromosomes. Proc. Natl. Acad. Sci. U.S.A. 93 (1996) 7137-7142
107. Tran H.G., Steger D.J., Iyer V.R., and Johnson A.D. The chromo domain protein chd1p from budding yeast is an ATP-dependent chromatin-modifying factor. EMBO J. 19 (2000) 2323-2331
108. Shen X., Mizuguchi G., Hamiche A., and Wu C. A chromatin remodelling complex involved in transcription and DNA processing. Nature 406 (2000) 541-544
109. Morrison A.J., Highland J., Krogan N.J., Arbel-Eden A., Greenblatt J.F., Haber J.E., and Shen X. INO80 and gamma-H2AX interaction links ATP-dependent chromatin remodeling to DNA damage repair. Cell 119 (2004) 767-775
110. van Attikum H., Fritsch O., Hohn B., and Gasser S.M. Recruitment of the INO80 complex by H2A phosphorylation links ATP-dependent chromatin remodeling with DNA double-strand break repair. Cell 119 (2004) 777-788
111. Rogakou E.P., Pilch D.R., Orr A.H., Ivanova V.S., and Bonner W.M. DNA double-stranded breaks induce histone H2AX phosphorylation on serine 139. J. Biol. Chem. 273 (1998) 5858-5868
112. Cairns B.R. Around the world of DNA damage INO80 days. Cell 119 (2004) 733-735
113. Korber P., and Horz W. SWRred not shaken; mixing the histones. Cell 117 (2004) 5-7
114. Owen-Hughes T., and Bruno M. Molecular biology. Breaking the silence. Science 303 (2004) 324-325
115. Krogan N.J., Keogh M.C., Datta N., Sawa C., Ryan O.W., Ding H., Haw R.A., Pootoolal J., Tong A., Canadien V., Richards D.P., Wu X., Emili A., Hughes T.R., Buratowski S., and Greenblatt J.F. A Snf2 family ATPase complex required for recruitment of the histone H2A variant Htz1. Mol. Cell 12 (2003) 1565-1576
116. Kobor M.S., Venkatasubrahmanyam S., Meneghini M.D., Gin J.W., Jennings J.L., Link A.J., Madhani H.D., and Rine J. A protein complex containing the conserved Swi2/Snf2-related ATPase Swr1p deposits histone variant H2A.Z into euchromatin. PLoS Biol. 2 (2004) E131
117. Mizuguchi G., Shen X., Landry J., Wu W.H., Sen S., and Wu C. ATP-driven exchange of histone H2AZ variant catalyzed by SWR1 chromatin remodeling complex. Science 303 (2004) 343-348
118. Meneghini M.D., Wu M., and Madhani H.D. Conserved histone variant H2A.Z protects euchromatin from the ectopic spread of silent heterochromatin. Cell 112 (2003) 725-736
119. Zhang H., Richardson D.O., Roberts D.N., Utley R., Erdjument-Bromage H., Tempst P., Cote J., and Cairns B.R. The Yaf9 component of the SWR1 and NuA4 complexes is required for proper gene expression, histone H4 acetylation, and Htz1 replacement near telomeres. Mol. Cell. Biol. 24 (2004) 9424-9436
120. Krogan N.J., Baetz K., Keogh M.C., Datta N., Sawa C., Kwok T.C., Thompson N.J., Davey M.G., Pootoolal J., Hughes T.R., Emili A., Buratowski S., Hieter P., and Greenblatt J.F. Regulation of chromosome stability by the histone H2A variant Htz1, the Swr1 chromatin remodeling complex, and the histone acetyltransferase NuA4. Proc. Natl. Acad. Sci. U.S.A. 101 (2004) 13513-13518
121. Li B., Pattenden S.G., Lee D., Gutierrez J., Chen J., Seidel C., Gerton J., and Workman J.L. Preferential occupancy of histone variant H2AZ at inactive promoters influences local histone modifications and chromatin remodeling. Proc. Natl. Acad. Sci. U.S.A. 102 (2005) 18385-18390
122. Wu W.H., Alami S., Luk E., Wu C.H., Sen S., Mizuguchi G., Wei D., and Wu C. Swc2 is a widely conserved H2AZ-binding module essential for ATP-dependent histone exchange. Nat. Struct. Mol. Biol. 12 (2005) 1064-1071
123. Babiarz J.E., Halley J.E., and Rine J. Telomeric heterochromatin boundaries require NuA4-dependent acetylation of histone variant H2A.Z in Saccharomyces cerevisiae. Genes Dev. 20 (2006) 700-710
124. Keogh M.C., Mennella T.A., Sawa C., Berthelet S., Krogan N.J., Wolek A., Podolny V., Carpenter L.R., Greenblatt J.F., Baetz K., and Buratowski S. The Saccharomyces cerevisiae histone H2A variant Htz1 is acetylated by NuA4. Genes Dev. 20 (2006) 660-665
125. Kassabov S.R., Zhang B., Persinger J., and Bartholomew B. SWI/SNF unwraps, slides, and rewraps the nucleosome. Mol. Cell 11 (2003) 391-403
126. Kassabov S.R., Henry N.M., Zofall M., Tsukiyama T., and Bartholomew B. High-resolution mapping of changes in histone-DNA contacts of nucleosomes remodeled by ISW2. Mol. Cell. Biol. 22 (2002) 7524-7534
127. Fan H.Y., He X., Kingston R.E., and Narlikar G.J. Distinct strategies to make nucleosomal DNA accessible. Mol. Cell 11 (2003) 1311-1322
128. Schwanbeck R., Xiao H., and Wu C. Spatial contacts and nucleosome step movements induced by the NURF chromatin remodeling complex. J. Biol. Chem. 279 (2004) 39933-39941
129. Zofall M., Persinger J., Kassabov S.R., and Bartholomew B. Chromatin remodeling by ISW2 and SWI/SNF requires DNA translocation inside the nucleosome. Nat. Struct. Mol. Biol. (2006)
130. Kagalwala M.N., Glaus B.J., Dang W., Zofall M., and Bartholomew B. Topography of the ISW2-nucleosome complex: insights into nucleosome spacing and chromatin remodeling. EMBO J. 23 (2004) 2092-2104
131. Watanabe H., Mizutani T., Haraguchi T., Yamamichi N., Minoguchi S., Yamamichi-Nishina M., Mori N., Kameda T., Sugiyama T., and Iba H. SWI/SNF complex is essential for NRSF-mediated suppression of neuronal genes in human nonsmall cell lung carcinoma cell lines. Oncogene 25 (2006) 470-479
132. Saha A., Wittmeyer J., and Cairns B.R. Chromatin remodeling through directional DNA translocation from an internal nucleosomal site. Nat. Struct. Mol. Biol. 12 (2005) 747-755
133. Strohner R., Wachsmuth M., Dachauer K., Mazurkiewicz J., Hochstatter J., Rippe K., and Langst G. A 'loop recapture' mechanism for ACF-dependent nucleosome remodeling. Nat. Struct. Mol. Biol. 12 (2005) 683-690
134. Deniss I.S., and Morgan A.R. Studies on the mechanism of DNA cleavage by ethidium. Nucleic Acids Res. 3 (1976) 315-323
135. Krishnamurthy G., Polte T., Rooney T., and Hogan M.E. A photochemical method to map ethidium bromide binding sites on DNA: application to a bent DNA fragment. Biochemistry 29 (1990) 981-988
136. Eberharter A., Ferrari S., Langst G., Straub T., Imhof A., Varga-Weisz P., Wilm M., and Becker P.B. Acf1, the largest subunit of CHRAC, regulates ISWI-induced nucleosome remodelling. EMBO J. 20 (2001) 3781-3788
137. LeRoy G., Orphanides G., Lane W.S., and Reinberg D. Requirement of RSF and FACT for transcription of chromatin templates in vitro. Science 282 (1998) 1900-1904
138. LeRoy G., Loyola A., Lane W.S., and Reinberg D. Purification and characterization of a human factor that assembles and remodels chromatin. J. Biol. Chem. 275 (2000) 14787-14790
139. Poot R.A., Dellaire G., Hulsmann B.B., Grimaldi M.A., Corona D.F., Becker P.B., Bickmore W.A., and Varga-Weisz P.D. HuCHRAC, a human ISWI chromatin remodelling complex contains hACF1 and two novel histone-fold proteins. EMBO J. 19 (2000) 3377-3387
140. Clapier C.R., Nightingale K.P., and Becker P.B. A critical epitope for substrate recognition by the nucleosome remodeling ATPase ISWI. Nucleic Acids Res. 30 (2002) 649-655
141. Loyola A., LeRoy G., Wang Y.H., and Reinberg D. Reconstitution of recombinant chromatin establishes a requirement for histone-tail modifications during chromatin assembly and transcription. Genes Dev. 15 (2001) 2837-2851
142. Li H., Ilin S., Wang W., Duncan E.M., Wysocka J., Allis C.D., and Patel D.J. Molecular basis for site-specific read-out of histone H3K4me3 by the BPTF PHD finger of NURF. Nature 442 (2006) 91-95
143. Wysocka J., Swigut T., Xiao H., Milne T.A., Kwon S.Y., Landry J., Kauer M., Tackett A.J., Chait B.T., Badenhorst P., Wu C., and Allis C.D. A PHD finger of NURF couples histone H3 lysine 4 trimethylation with chromatin remodelling. Nature 442 (2006) 86-90
144. Santos-Rosa H., Schneider R., Bernstein B.E., Karabetsou N., Morillon A., Weise C., Schreiber S.L., Mellor J., and Kouzarides T. Methylation of histone H3 K4 mediates association of the Isw1p ATPase with chromatin. Mol. Cell 12 (2003) 1325-1332
145. Hassan A.H., Neely K.E., and Workman J.L. Histone acetyltransferase complexes stabilize swi/snf binding to promoter nucleosomes. Cell 104 (2001) 817-827
146. Agalioti T., Chen G., and Thanos D. Deciphering the transcriptional histone acetylation code for a human gene. Cell 111 (2002) 381-392
147. Huang Z.Q., Li J., Sachs L.M., Cole P.A., and Wong J. A role for cofactor-cofactor and cofactor-histone interactions in targeting p300, SWI/SNF and Mediator for transcription. EMBO J. 22 (2003) 2146-2155
148. Henderson A., Holloway A., Reeves R., and Tremethick D.J. Recruitment of SWI/SNF to the human immunodeficiency virus type 1 promoter. Mol. Cell. Biol. 24 (2004) 389-397
149. Geng F., and Laurent B.C. Roles of SWI/SNF and HATs throughout the dynamic transcription of a yeast glucose-repressible gene. EMBO J. 23 (2004) 127-137
150. Xu F., Zhang K., and Grunstein M. Acetylation in histone H3 globular domain regulates gene expression in yeast. Cell 121 (2005) 375-385
151. Duina A.A., and Winston F. Analysis of a mutant histone H3 that perturbs the association of Swi/Snf with chromatin. Mol. Cell. Biol. 24 (2004) 561-572
152. Logie C., Tse C., Hansen J.C., and Peterson C.L. The core histone N-terminal domains are required for multiple rounds of catalytic chromatin remodeling by the SWI/SNF and RSC complexes. Biochemistry 38 (1999) 2514-2522