Chapter 5 Nuclear Actin-Related Proteins in Epigenetic Control

International Review of Cell and Molecular Biology

Volumn 277, Issue C, 2009, Pages 157-215

  Meagher, Richard B ^a   Kandasamy, Muthugapatti K ^a   McKinney, Elizabeth C ^a   Roy, Eileen ^a  

^a University of Georgia   (United States)

Author keywords

ARPs; Chromatin remodeling; Epigenetic control; Histone variant; INO80; Multicellular development; Nucleosome; SWI SNF; SWR1

Indexed keywords

ACTIN; ACTIN RELATED PROTEIN; ACTIN RELATED PROTEIN 2; ACTIN RELATED PROTEIN 3; ACTIN RELATED PROTEIN 4; ACTIN RELATED PROTEIN 5; ACTIN RELATED PROTEIN 6; ACTIN RELATED PROTEIN 7; ACTIN RELATED PROTEIN 8; ACTIN RELATED PROTEIN 9; ADENOSINE TRIPHOSPHATASE; AGOUTI PROTEIN; DNA; MYC PROTEIN; NUCLEAR PROTEIN; PROTEIN P53; TATA BINDING PROTEIN; TRANSCRIPTION FACTOR SNF; UNCLASSIFIED DRUG;

APOPTOSIS; ARABIDOPSIS; BIOCHEMISTRY; CELL AGING; CELL CYCLE REGULATION; CELL MATURATION; CELL NUCLEUS; CELL PROLIFERATION; CHROMATIN ASSEMBLY AND DISASSEMBLY; CYTOLOGY; DICTYOSTELIUM DISCOIDEUM; DNA REPAIR; DNA STRUCTURE; DNA TRANSCRIPTION; EPIGENETICS; EUKARYOTE; GENE EXPRESSION REGULATION; GENE SILENCING; GENETIC ANALYSIS; GENETIC CONSERVATION; GENETIC REGULATION; HUMAN; MACROMOLECULE; MALIGNANT NEOPLASTIC DISEASE; MALIGNANT TRANSFORMATION; NONHUMAN; NUCLEAR EXPORT SIGNAL; ORGANOGENESIS; OVARY POLYCYSTIC DISEASE; PHYLOGENY; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN FUNCTION; PROTEIN LOCALIZATION; PROTEIN STRUCTURE; PROTEIN TRANSPORT; REPRODUCTION; REVIEW; SACCHAROMYCES CEREVISIAE; SEQUENCE HOMOLOGY; SPECIES DIFFERENCE; ANIMAL; CHEMISTRY; CHROMATIN; GENETIC EPIGENESIS; GENETICS; METABOLISM;

ANIMALIA; EUKARYOTA;

ACTINS; ANIMALS; CHROMATIN; EPIGENESIS, GENETIC; HUMANS; NUCLEAR PROTEINS;

EID: 70349783837     PISSN: 19376448     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S1937-6448(09)77005-4     Document Type: Review

References (257)

1. Adam R.D. The Giardia lamblia genome. Int. J. Parasitol. 30 (2000) 475-484
2. Adam M., Robert F., Larochelle M., and Gaudreau L. H2A.Z is required for global chromatin integrity and for recruitment of RNA polymerase II under specific conditions. Mol. Cell. Biol. 21 (2001) 6270-6279
3. Adams P.D. Remodeling chromatin for senescence. Aging Cell 6 (2007) 425-427
4. Adams P.D. Remodeling of chromatin structure in senescent cells and its potential impact on tumor suppression and aging. Gene 397 (2007) 84-93
5. Adl S.M., Leander B.S., Simpson A.G., Archibald J.M., Anderson O.R., Bass D., et al. Diversity, nomenclature, and taxonomy of protists. Syst. Biol. 56 (2007) 684-689
6. Ae K., Kobayashi N., Sakuma R., Ogata T., Kuroda H., Kawaguchi N., et al. Chromatin remodeling factor encoded by ini1 induces G1 arrest and apoptosis in ini1-deficient cells. Oncogene 21 (2002) 3112-3120
7. Aoyama N., Oka A., Kitayama K., Kurumizaka H., and Harata M. The actin-related protein hArp8 accumulates on the mitotic chromosomes and functions in chromosome alignment. Exp. Cell Res. 314 (2008) 859-868
8. Aparicio S., Chapman J., Stupka E., Putnam N., Chia J.M., Dehal P., et al. Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Science 297 (2002) 1301-1310
9. Auger A., Galarneau L., Altaf M., Nourani A., Doyon Y., Utley R.T., et al. Eaf1 is the platform for NuA4 molecular assembly that evolutionarily links chromatin acetylation to ATP-dependent exchange of histone H2A variants. Mol. Cell. Biol. 28 (2008) 2257-2270
10. Bak P., and Paczuski M. Complexity, contingency, and criticality. Proc. Natl. Acad. Sci. USA 92 (1995) 6689-6696
11. Barak O., Lazzaro M.A., Cooch N.S., Picketts D.J., and Shiekhattar R. A tissue-specific, naturally occurring human SNF2L variant inactivates chromatin remodeling. J. Biol. Chem. 279 (2004) 45130-45138
12. Bartee L., and Bender J. Two Arabidopsis methylation-deficiency mutations confer only partial effects on a methylated endogenous gene family. Nucleic Acids Res. 29 (2001) 2127-2134
13. Bendich A.J., and Drlica K. Prokaryotic and eukaryotic chromosomes: what's the difference?. Bioessays 22 (2000) 481-486
14. Bezhani S., Winter C., Hershman S., Wagner J.D., Kennedy J.F., Kwon C.S., et al. Unique, shared, and redundant roles for the Arabidopsis SWI/SNF chromatin remodeling ATPases BRAHMA and SPLAYED. Plant Cell 19 (2007) 403-416
15. Bird A.W., Yu D.Y., Pray-Grant M.G., Qiu Q., Harmon K.E., Megee P.C., et al. Acetylation of histone H4 by Esa1 is required for DNA double-strand break repair. Nature 419 (2002) 411-415
16. Bjornsson H.T., Fallin M.D., and Feinberg A.P. An integrated epigenetic and genetic approach to common human disease. Trends Genet. 20 (2004) 350-358
17. Bleecker A.B., and Patterson S.E. Last exit: senescence, abscission, and meristem arrest in Arabidopsis. Plant Cell 9 (1997) 1169-1179
18. Blessing C.A., Ugrinova G.T., and Goodson H.V. Actin and ARPs: action in the nucleus. Trends Cell Biol. 14 (2004) 435-442
19. Bottardi S., Aumont A., Grosveld F., and Milot E. Developmental stage-specific epigenetic control of human beta-globin gene expression is potentiated in hematopoietic progenitor cells prior to their transcriptional activation. Blood 102 (2003) 3989-3997
20. Boyer L.A., and Peterson C.L. Actin-related proteins (Arps): conformational switches for chromatin-remodeling machines?. Bioessays 22 (2000) 666-672
21. Brannian J.D., Eyster K.M., Weber M., and Diggins M. Pioglitazone administration alters ovarian gene expression in aging obese lethal yellow mice. Reprod. Biol. Endocrinol. 6 (2008) 10
22. Brown E., Malakar S., and Krebs J.E. How many remodelers does it take to make a brain? Diverse and cooperative roles of ATP-dependent chromatin-remodeling complexes in development. Biochem. Cell Biol. 85 (2007) 444-462
23. Brzeski J., and Jerzmanowski A. Deficient in DNA methylation 1 (DDM1) defines a novel family of chromatin-remodeling factors. J. Biol. Chem. 278 (2003) 823-828
24. Burzynski S.R. Aging: gene silencing or gene activation?. Med. Hypotheses 64 (2005) 201-208
25. Cai Y., Jin J., Florens L., Swanson S.K., Kusch T., Li B., et al. The mammalian YL1 protein is a shared subunit of the TRRAP/TIP60 histone acetyltransferase and SRCAP complexes. J. Biol. Chem. 280 (2005) 13665-13670
26. Cai Y., Jin J., Gottschalk A.J., Yao T., Conaway J.W., and Conaway R.C. Purification and assay of the human INO80 and SRCAP chromatin remodeling complexes. Methods 40 (2006) 312-317
27. Cairns B.R. Around the world of DNA damage INO80 days. Cell 119 (2004) 733-735
28. Cairns B.R., Erdjument-Bromage H., Tempst P., Winston F., and Kornberg R.D. Two actin-related proteins are shared functional components of the chromatin-remodeling complexes RSC and SWI/SNF. Mol. Cell 2 (1998) 639-651
29. Champion K., and Higgins N.P. Growth rate toxicity phenotypes and homeostatic supercoil control differentiate Escherichia coli from Salmonella enterica serovar Typhimurium. J. Bacteriol. 189 (2007) 5839-5849
30. Chan H.M., Narita M., Lowe S.W., and Livingston D.M. The p400 E1A-associated protein is a novel component of the p53-> p21 senescence pathway. Genes Dev. 19 (2005) 196-201
31. Chang C., Kwok S.F., Bleecker A.B., and Meyerowitz E.M. Arabidopsis ethylene-response gene ETR1: similarity of product to two-component regulators. Science 262 (1993) 539-544
32. Chen Z.J. Genetic and epigenetic mechanisms for gene expression and phenotypic variation in plant polyploids. Annu. Rev. Plant Biol. 58 (2007) 377-406
33. Chen M., and Shen X. Nuclear actin and actin-related proteins in chromatin dynamics. Curr. Opin. Cell Biol. 19 (2007) 326-330
34. Chen Z., Tan J.L., Ingouff M., Sundaresan V., and Berger F. Chromatin assembly factor 1 regulates the cell cycle but not cell fate during male gametogenesis in Arabidopsis thaliana. Development 135 (2008) 65-73
35. Chi T.H., Wan M., Zhao K., Taniuchi I., Chen L., Littman D.R., et al. Reciprocal regulation of CD4/CD8 expression by SWI/SNF-like BAF complexes. Nature 418 (2002) 195-199
36. Choi E.Y., Park J.A., Sung Y.H., and Kwon H. Generation of the dominant-negative mutant of hArpNbeta: a component of human SWI/SNF chromatin remodeling complex. Exp. Cell Res. 271 (2001) 180-188
37. Choi K., Kim S., Kim S.Y., Kim M., Hyun Y., Lee H., et al. SUPPRESSOR OF FRIGIDA3 encodes a nuclear ACTIN-RELATED PROTEIN6 required for floral repression in Arabidopsis. Plant Cell 17 (2005) 2647-2660
38. Choi K., Park C., Lee J., Oh M., Noh B., and Lee I. Arabidopsis homologs of components of the SWR1 complex regulate flowering and plant development. Development 134 (2007) 1931-1941
39. Conaway R.C., and Conaway J.W. The INO80 chromatin remodeling complex in transcription, replication and repair. Trends Biochem. Sci. 34 (2009) 71-77
40. Crapper D.R., Quittkat S., and de Boni U. Altered chromatin conformation in Alzheimer's disease. Brain 102 (1979) 483-495
41. Csink A.K., and Henikoff S. Genetic modification of heterochromatic association and nuclear organization in Drosophila. Nature 381 (1996) 529-531
42. Cuzin F., Grandjean V., and Rassoulzadegan M. Inherited variation at the epigenetic level: paramutation from the plant to the mouse. Curr. Opin. Genet Dev. 18 (2008) 193-196
43. Dang W., and Bartholomew B. Domain architecture of the catalytic subunit in the ISW2-nucleosome complex. Mol. Cell. Biol. 27 (2007) 8306-8317
44. Deal R.B., Kandasamy M.K., McKinney E.C., and Meagher R.B. The nuclear actin-related protein ARP6 is a pleiotropic developmental regulator required for the maintenance of FLOWERING LOCUS C expression and repression of flowering in Arabidopsis. Plant Cell 17 (2005) 2633-2646
45. Deal R.B., Topp C.N., McKinney E.C., and Meagher R.B. Repression of flowering in Arabidopsis requires activation of FLOWERING LOCUS C expression by the histone variant H2A.Z. Plant Cell 19 (2007) 74-83
46. Debril M.B., Gelman L., Fayard E., Annicotte J.S., Rocchi S., and Auwerx J. Transcription factors and nuclear receptors interact with the SWI/SNF complex through the BAF60c subunit. J. Biol. Chem. 279 (2004) 16677-16686
47. DeCristofaro M.F., Betz B.L., Wang W., and Weissman B.E. Alteration of hSNF5/INI1/BAF47 detected in rhabdoid cell lines and primary rhabdomyosarcomas but not Wilms' tumors. Oncogene 18 (1999) 7559-7565
48. 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
49. Dinant C., Houtsmuller A.B., and Vermeulen W. Chromatin structure and DNA damage repair. Epigen. Chrom. 1 (2008) 9
50. Dirscherl S.S., and Krebs J.E. Functional diversity of ISWI complexes. Biochem. Cell Biol. 82 (2004) 482-489
51. Downs J.A., Allard S., Jobin-Robitaille O., Javaheri A., Auger A., Bouchard N., et al. Binding of chromatin-modifying activities to phosphorylated histone H2A at DNA damage sites. Mol. Cell 16 (2004) 979-990
52. Dryhurst D., Thambirajah A.A., and Ausio J. New twists on H2A.Z: a histone variant with a controversial structural and functional past. Biochem. Cell Biol. 82 (2004) 490-497
53. Ebbert R., Birkmann A., and Schuller H.J. The product of the SNF2/SWI2 paralogue INO80 of Saccharomyces cerevisiae required for efficient expression of various yeast structural genes is part of a high-molecular-weight protein complex. Mol. Microbiol. 32 (1999) 741-751
54. Eckley D.M., and Schroer T.A. Interactions between the evolutionarily conserved, actin-related protein, Arp11, actin, and Arp1. Mol. Biol. Cell 14 (2003) 2645-2654
55. Eckley D.M., Gill S.R., Melkonian K.A., Bingham J.B., Goodson H.V., Heuser J.E., et al. Analysis of dynactin subcomplexes reveals a novel actin-related protein associated with the arp1 minifilament pointed end. J. Cell Biol. 147 (1999) 307-320
56. Elango N., Kim S.H., Vigoda E., and Yi S.V. Mutations of different molecular origins exhibit contrasting patterns of regional substitution rate variation. PLoS Comput. Biol. 4 (2008) e1000015
57. Fan J.Y., Rangasamy D., Luger K., and Tremethick D.J. H2A.Z alters the nucleosome surface to promote HP1alpha-mediated chromatin fiber folding. Mol. Cell 16 (2004) 655-661
58. Feng Y., Lee N., and Fearon E.R. TIP49 regulates beta-catenin-mediated neoplastic transformation and T-cell factor target gene induction via effects on chromatin remodeling. Cancer Res. 63 (2003) 8726-8734
59. Ferluga J. Possible organ and age-related epigenetic factors in Huntington's disease and colorectal carcinoma. Med. Hypotheses 29 (1989) 51-54
60. Ford J., Odeyale O., and Shen C.H. Activator-dependent recruitment of SWI/SNF and INO80 during INO1 activation. Biochem. Biophys. Res. Commun. 373 (2008) 602-606
61. Fraga M.F., Agrelo R., and Esteller M. Cross-talk between aging and cancer: the epigenetic language. Ann. NY Acad. Sci. 1100 (2007) 60-74
62. Francis D. The plant cell cycle-15 years on. New Phytol. 174 (2007) 261-278
63. Frankel S., Sigel E.A., Craig C., Elgin S.C., Mooseker M.S., and Artavanis-Tsakonas S. An actin-related protein in Drosophila colocalizes with heterochromatin protein 1 in pericentric heterochromatin. J. Cell Sci. 110 Pt 17 (1997) 1999-2012
64. Fritsch O., Benvenuto G., Bowler C., Molinier J., and Hohn B. The INO80 protein controls homologous recombination in Arabidopsis thaliana. Mol. Cell 16 (2004) 479-485
65. Fuchs M., Gerber J., Drapkin R., Sif S., Ikura T., Ogryzko V., et al. The p400 complex is an essential E1A transformation target. Cell 106 (2001) 297-307
66. Fujii K., Yonemasu Y., Kitamura K., and Tsubota Y. A genetic aspect of chromatin proteins of human brain tumors. J. Neurol. 223 (1980) 23-34
67. Galarneau L., Nourani A., Boudreault A.A., Zhang Y., Heliot L., Allard S., et al. Multiple links between the NuA4 histone acetyltransferase complex and epigenetic control of transcription. Mol. Cell 5 (2000) 927-937
68. Galkin V.E., VanLoock M.S., Orlova A., and Egelman E.H. A new internal mode in F-actin helps explain the remarkable evolutionary conservation of actin's sequence and structure. Curr. Biol. 12 (2002) 570-575
69. Garcia B.A., Busby S.A., Shabanowitz J., Hunt D.F., and Mishra N. Resetting the epigenetic histone code in the MRL-lpr/lpr mouse model of lupus by histone deacetylase inhibition. J. Proteome Res. 4 (2005) 2032-2042
70. 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
71. Georgieva M., Harata M., and Miloshev G. The nuclear actin-related protein Act3p/Arp4 influences yeast cell shape and bulk chromatin organization. J. Cell Biochem. 104 (2008) 59-67
72. Gong F., Fahy D., Liu H., Wang W., and Smerdon M.J. Role of the mammalian SWI/SNF chromatin remodeling complex in the cellular response to UV damage. Cell Cycle 7 (2008) 1067-1074
73. Goodson H.V., and Hawse W.F. Molecular evolution of the actin family. J. Cell Sci. 115 (2002) 2619-2622
74. Gordon J.L., and Sibley L.D. Comparative genome analysis reveals a conserved family of actin-like proteins in apicomplexan parasites. BMC Genom. 6 (2005) 179
75. Gordon J.L., Beatty W.L., and Sibley L.D. A novel actin-related protein is associated with daughter cell formation in Toxoplasma gondii. Eukaryot. Cell 7 (2008) 1500-1512
76. Gorzer I., Schuller C., Heidenreich E., Krupanska L., Kuchler K., and Wintersberger U. The nuclear actin-related protein Act3p/Arp4p of Saccharomyces cerevisiae is involved in transcription regulation of stress genes. Mol. Microbiol. 50 (2003) 1155-1171
77. Graff J., and Mansuy I.M. Epigenetic codes in cognition and behaviour. Behav. Brain Res. 192 (2008) 70-87
78. Grewal S.I., and Moazed D. Heterochromatin and epigenetic control of gene expression. Science 301 (2003) 798-802
79. Groth A., Rocha W., Verreault A., and Almouzni G. Chromatin challenges during DNA replication and repair. Cell 128 (2007) 721-733
80. Groudine M., Kohwi-Shigematsu T., Gelinas R., Stamatoyannopoulos G., and Papayannopoulou T. Human fetal to adult hemoglobin switching: changes in chromatin structure of the beta-globin gene locus. Proc. Natl. Acad. Sci. USA 80 (1983) 7551-7555
81. Haig D. The (dual) origin of epigenetics. Cold Spring Harb. Symp. Quant. Biol. 69 (2004) 67-70
82. Harata M., Karwan A., and Wintersberger U. An essential gene of Saccharomyces cerevisiae coding for an actin-related protein. Proc. Natl. Acad. Sci. USA 91 (1994) 8258-8262
83. Harata M., Mochizuki R., and Mizuno S. Two isoforms of a human actin-related protein show nuclear localization and mutually selective expression between brain and other tissues. Biosci. Biotechnol. Biochem. 63 (1999) 917-923
84. Harata M., Oma Y., Mizuno S., Jiang Y.W., Stillman D.J., and Wintersberger U. The nuclear actin-related protein of Saccharomyces cerevisiae, Act3p/Arp4, interacts with core histones. Mol. Biol. Cell 10 (1999) 2595-2605
85. Harata M., Oma Y., Tabuchi T., Zhang Y., Stillman D.J., and Mizuno S. Multiple actin-related proteins of Saccharomyces cerevisiae are present in the nucleus. J. Biochem. (Tokyo) 128 (2000) 665-671
86. Harata M., Nishimori K., and Hatta S. Identification of two cDNAs for human actin-related proteins (Arps) that have remarkable similarity to conventional actin. Biochim. Biophys. Acta 1522 (2001) 130-133
87. Harata M., Zhang Y., Stillman D.J., Matsui D., Oma Y., Nishimori K., et al. Correlation between chromatin association and transcriptional regulation for the Act3p/Arp4 nuclear actin-related protein of Saccharomyces cerevisiae. Nucleic Acids Res. 30 (2002) 1743-1750
88. Harries P.A., Pan A., and Quatrano R.S. Actin-related protein2/3 complex component ARPC1 is required for proper cell morphogenesis and polarized cell growth in Physcomitrella patens. Plant Cell 17 (2005) 2327-2339
89. Hedges S.B., Blair J.E., Venturi M.L., and Shoe J.L. A molecular timescale of eukaryote evolution and the rise of complex multicellular life. BMC Evol. Biol. 4 (2004) 2
90. Henderson I.R., and Jacobsen S.E. Epigenetic inheritance in plants. Nature 447 (2007) 418-424
91. Henikoff S. Position effects and variegation enhancers in an autosomal region of Drosophila melanogaster. Genetics 93 (1979) 105-115
92. Huanca-Mamani W., Garcia-Aguilar M., Leon-Martinez G., Grossniklaus U., and Vielle-Calzada J.P. CHR11, a chromatin-remodeling factor essential for nuclear proliferation during female gametogenesis in Arabidopsis thaliana. Proc. Natl. Acad. Sci. USA 102 (2005) 17231-17236
93. Huang M.E., Souciet J.L., Chuat J.C., and Galibert F. Identification of ACT4, a novel essential actin-related gene in the yeast Saccharomyces cerevisiae. Yeast 12 (1996) 839-848
94. Ikura T., Ogryzko V.V., Grigoriev M., Groisman R., Wang J., Horikoshi M., et al. Involvement of the TIP60 histone acetylase complex in DNA repair and apoptosis. Cell 102 (2000) 463-473
95. Iyer L.M., Anantharaman V., Wolf M.Y., and Aravind L. Comparative genomics of transcription factors and chromatin proteins in parasitic protists and other eukaryotes. Int. J. Parasitol. 38 (2008) 1-31
96. Jeddeloh J.A., Stokes T.L., and Richards E.J. Maintenance of genomic methylation requires a SWI2/SNF2-like protein. Nat. Genet. 22 (1999) 94-97
97. Jehn B.M., and Osborne B.A. Gene regulation associated with apoptosis. Crit. Rev. Eukaryot. Gene Exp. 7 (1997) 179-193
98. Jiang Y.W., and Stillman D.J. Epigenetic effects on yeast transcription caused by mutations in an actin-related protein present in the nucleus. Genes Dev. 10 (1996) 604-619
99. Jin J., Cai Y., Yao T., Gottschalk A.J., Florens L., Swanson S.K., et al. A mammalian chromatin remodeling complex with similarities to the yeast INO80 complex. J. Biol. Chem. 280 (2005) 41207-41212
100. Jirtle R.L., Sander M., and Barrett J.C. Genomic imprinting and environmental disease susceptibility. Environ. Health Perspect. 108 (2000) 271-278
101. Johnson L., Cao X., and Jacobsen S. Interplay between two epigenetic marks. DNA methylation and histone H3 lysine 9 methylation. Curr. Biol. 12 (2002) 1360-1367
102. Jonsson Z.O., Jha S., Wohlschlegel J.A., and Dutta A. Rvb1p/Rvb2p recruit Arp5p and assemble a functional Ino80 chromatin remodeling complex. Mol. Cell 16 (2004) 465-477
103. Kandasamy M.K., McKinney E.C., and Meagher R.B. Cell cycle-dependent association of Arabidopsis actin-related proteins AtARP4 and AtARP7 with the nucleus. Plant J. 33 (2003) 939-948
104. Kandasamy M.K., Deal R.B., McKinney E.C., and Meagher R.B. Plant actin-related proteins. Trends Plant Sci. 9 (2004) 196-202
105. Kandasamy M.K., Deal R.B., McKinney E.C., and Meagher R.B. Silencing the nuclear actin-related protein AtARP4 in Arabidopsis has multiple effects on plant development, including early flowering and delayed floral senescence. Plant J. 41 (2005) 845-858
106. Kandasamy M.K., McKinney E.C., Deal R.B., and Meagher R.B. Arabidopsis ARP7 is an essential actin-related protein required for normal embryogenesis, plant architecture, and floral organ abscission. Plant Physiol. 138 (2005) 2019-2032
107. Kandasamy M.K., McKinney E.C., and Meagher R.B. ACTIN-RELATED PROTEIN8 encodes an F-box protein localized to the nucleolus in Arabidopsis. Plant Cell Physiol. 49 (2008) 858-863
108. Kandasamy M.K., McKinney L.C., Deal R.B., Smith A.P., and Meagher R.B. Arabidopsis actin-related protein ARP5 in multicellular development and DNA repair (2009), Developmental Biology (In Press)
109. Kanno T., Mette M.F., Kreil D.P., Aufsatz W., Matzke M., and Matzke A.J. Involvement of putative SNF2 chromatin remodeling protein DRD1 in RNA-directed DNA methylation. Curr. Biol. 14 (2004) 801-805
110. Kato M., Sasaki M., Mizuno S., and Harata M. Novel actin-related proteins in vertebrates: similarities of structure and expression pattern to Arp6 localized on Drosophila heterochromatin. Gene 268 (2001) 133-140
111. Kawashima S., Ogiwara H., Tada S., Harata M., Wintersberger U., Enomoto T., et al. The INO80 complex is required for damage-induced recombination. Biochem. Biophys. Res. Commun. 355 (2007) 835-841
112. Kehrer-Sawatzki H., and Cooper D.N. Understanding the recent evolution of the human genome: insights from human-chimpanzee genome comparisons. Hum. Mutat. 28 (2007) 99-130
113. Kitayama K., Kamo M., Oma Y., Matsuda R., Uchida T., Ikura T., et al. The human actin-related protein hArp5: nucleo-cytoplasmic shuttling and involvement in DNA repair. Exp. Cell Res. 315 (2009) 206-217
114. Klar A.J. Lessons learned from studies of fission yeast mating-type switching and silencing. Annu. Rev. Genet. 41 (2007) 213-236
115. Klee H.J. Control of ethylene-mediated processes in tomato at the level of receptors. J. Exp. Bot. 53 (2002) 2057-2063
116. Klochendler-Yeivin A., Picarsky E., and Yaniv M. Increased DNA damage sensitivity and apoptosis in cells lacking the Snf5/Ini1 subunit of the SWI/SNF chromatin remodeling complex. Mol. Cell. Biol. 26 (2006) 2661-2674
117. Kobor M.S., Venkatasubrahmanyam S., Meneghini M.D., Gin J.W., Jennings J.L., Link A.J., et al. A protein complex containing the conserved Swi2/Snf2-related ATPase Swr1p deposits histone variant H2A.Z into euchromatin. PLoS Biol. 2 (2004) E131
118. Krogan N.J., Keogh M.C., Datta N., Sawa C., Ryan O.W., Ding H., et al. A Snf2 family ATPase complex required for recruitment of the histone H2A variant Htz1. Mol. Cell. 12 (2003) 1565-1576
119. Kuo L.J., and Yang L.X. Gamma-H2AX-a novel biomarker for DNA double-strand breaks. In Vivo 22 (2008) 305-309
120. Kuroda Y., Oma Y., Nishimori K., Ohta T., and Harata M. Brain-specific expression of the nuclear actin-related protein ArpNalpha and its involvement in mammalian SWI/SNF chromatin remodeling complex. Biochem. Biophys. Res. Commun. 299 (2002) 328-334
121. Kwon C.S., and Wagner D. Unwinding chromatin for development and growth: a few genes at a time. Trends Genet. 23 (2007) 403-412
122. Larochelle M., and Gaudreau L. H2A.Z has a function reminiscent of an activator required for preferential binding to intergenic DNA. Embo. J. 22 (2003) 4512-4522
123. Lazaro A., Gomez-Zambrano A., Lopez-Gonzalez L., Pineiro M., and Jarillo J.A. Mutations in the Arabidopsis SWC6 gene, encoding a component of the SWR1 chromatin remodelling complex, accelerate flowering time and alter leaf and flower development. J. Exp. Bot. 59 (2008) 653-666
124. Lee J.H., Chang S.H., Shim J.H., Lee J.Y., Yoshida M., and Kwon H. Cytoplasmic localization and nucleo-cytoplasmic shuttling of BAF53, a component of chromatin-modifying complexes. Mol. Cells 16 (2003) 78-83
125. Lee J.H., Lee J.Y., Chang S.H., Kang M.J., and Kwon H. Effects of Ser2 and Tyr6 mutants of BAF53 on cell growth and p53-dependent transcription. Mol. Cells 19 (2005) 289-293
126. Lee K., Kang M.J., Kwon S.J., Kwon Y.K., Kim K.W., Lim J.H., et al. Expansion of chromosome territories with chromatin decompaction in BAF53-depleted interphase cells. Mol. Biol. Cell 18 (2007) 4013-4023
127. Lee K., Shim J.H., Kang M.J., Kim J.H., Ahn J.S., Yoo S.J., et al. Association of BAF53 with mitotic chromosomes. Mol. Cells 24 (2007) 288-293
128. Lessard J., Wu J.I., Ranish J.A., Wan M., Winslow M.M., Staahl B.T., et al. An essential switch in subunit composition of a chromatin remodeling complex during neural development. Neuron 55 (2007) 201-215
129. Lewis M.W., Leslie M.E., and Liljegren S.J. Plant separation: 50 ways to leave your mother. Curr. Opin. Plant Biol. 9 (2006) 59-65
130. Li B., Pattenden S.G., Lee D., Gutierrez J., Chen J., Seidel C., et al. Preferential occupancy of histone variant H2AZ at inactive promoters influences local histone modifications and chromatin remodeling. Proc. Natl. Acad. Sci. USA 102 (2005) 18385-18390
131. Lickert H., Takeuchi J.K., Von Both I., Walls J.R., McAuliffe F., Adamson S.L., et al. Baf60c is essential for function of BAF chromatin remodelling complexes in heart development. Nature 432 (2004) 107-112
132. Lin H.Y., Chen C.S., Lin S.P., and Weng J.R. Targeting histone deacetylase in cancer therapy. Med. Res. Rev. 26 (2006) 397-413
133. Linger J.G., and Tyler J.K. Chromatin disassembly and reassembly during DNA repair. Mutat. Res. 618 (2007) 52-64
134. Liu R., Liu H., Chen X., Kirby M., Brown P.O., and Zhao K. Regulation of CSF1 promoter by the SWI/SNF-like BAF complex. Cell 106 (2001) 309-318
135. March-Diaz R., Garcia-Dominguez M., Florencio F.J., and Reyes J.C. SEF, a new protein required for flowering repression in Arabidopsis, interacts with PIE1 and ARP6. Plant Physiol. 143 (2007) 893-901
136. Martin-Trillo M., Lazaro A., Poethig R.S., Gomez-Mena C., Pineiro M.A., Martinez-Zapater J.M., et al. EARLY IN SHORT DAYS 1 (ESD1) encodes ACTIN-RELATED PROTEIN 6 (AtARP6), a putative component of chromatin remodelling complexes that positively regulates FLC accumulation in Arabidopsis. Development 133 (2006) 1241-1252
137. McKinney E.C., Kandasamy M.K., and Meagher R.B. Arabidopsis contains ancient classes of differentially expressed actin-related protein genes. Plant Physiol. 128 (2002) 997-1007
138. Meagher R.B. The impact of historical contingency on gene phylogeny: plant actin diversity. In: Hecht M., MacIntyre R., and Clegg M. (Eds). Evolutionary Biology, 28 (1995), NY, Plenum Press 195-215
139. Meagher R.B., McKinney E.C., and Kandasamy M.K. Isovariant dynamics expand and buffer the responses of complex systems: the diverse plant actin gene family. Plant Cell 11 (1999) 995-1006
140. Meagher R.B., McKinney E.C., and Vitale A.V. The evolution of new structures: clues from plant cytoskeletal genes. Trends Genet. 15 (1999) 278-284
141. Meagher R.B., Deal R.B., Kandasamy M.K., and McKinney E.C. Nuclear actin-related proteins as epigenetic regulators of development. Plant Physiol. 139 (2005) 1576-1585
142. Meagher R.B., Kandasamy M.K., Deal R.B., and McKinney E.C. Actin-related proteins in chromatin-level control of the cell cycle and developmental transitions. Trends Cell Biol. 17 (2007) 325-332
143. Meagher R.B., Kandasamy M.K., and McKinney E.C. Multicellular development and protein-protein interactions. Plant Signal Behav. 3 (2008) 333-336
144. Mehler M.F. Epigenetic principles and mechanisms underlying nervous system functions in health and disease. Prog. Neurobiol. 86 (2008) 305-341
145. Mehler M.F. Epigenetics and the nervous system. Ann. Neurol. 64 (2008) 602-617
146. Mehler M.F., and Purpura D.P. Autism, fever, epigenetics and the locus coeruleus. Brain Res. Rev 59 (2008) 388-392
147. 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
148. Metivier R., Penot G., Hubner M.R., Reid G., Brand H., Kos M., et al. Estrogen receptor-alpha directs ordered, cyclical, and combinatorial recruitment of cofactors on a natural target promoter. Cell 115 (2003) 751-763
149. Minoda A., Saitoh S., Takahashi K., and Toda T. BAF53/Arp4 homolog Alp5 in fission yeast is required for histone H4 acetylation, kinetochore-spindle attachment, and gene silencing at centromere. Mol. Biol. Cell 16 (2005) 316-327
150. Minucci S., and Pelicci P.G. Retinoid receptors in health and disease: co-regulators and the chromatin connection. Semin. Cell Dev. Biol. 10 (1999) 215-225
151. Mittelsten Scheid O., and Paszkowski J. Transcriptional gene silencing mutants. Plant Mol. Biol. 43 (2000) 235-241
152. Miura A., Yonebayashi S., Watanabe K., Toyama T., Shimada H., and Kakutani T. Mobilization of transposons by a mutation abolishing full DNA methylation in Arabidopsis. Nature 411 (2001) 212-214
153. 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
154. Mohrmann L., and Verrijzer C.P. Composition and functional specificity of SWI2/SNF2 class chromatin remodeling complexes. Biochim. Biophys. Acta 1681 (2005) 59-73
155. Morgan H.D., Sutherland H.G., Martin D.I., and Whitelaw E. Epigenetic inheritance at the agouti locus in the mouse. Nat. Genet. 23 (1999) 314-318
156. Morrison A.J., and Shen X. Chromatin modifications in DNA repair. Results Probl. Cell Differ. 41 (2006) 109-125
157. Morrison A.J., Highland J., Krogan N.J., Arbel-Eden A., Greenblatt J.F., Haber J.E., et al. INO80 and gamma-H2AX interaction links ATP-dependent chromatin remodeling to DNA damage repair. Cell 119 (2004) 767-775
158. Muller G.B., and Newman S.A. The innovation triad: an EvoDevo agenda. J. Exp. Zool. B Mol. Dev. Evol. 304 (2005) 487-503
159. Muller J., Oma Y., Vallar L., Friederich E., Poch O., and Winsor B. Sequence and comparative genomic analysis of actin-related proteins. Mol. Biol. Cell 16 (2005) 5736-5748
160. Nanney D.L. Epigenetic control systems. Proc. Natl. Acad. Sci. USA 44 (1958) 712-717
161. Napolitano M.A., Cipollaro M., Cascino A., Melone M.A., Giordano A., and Galderisi U. Brg1 chromatin remodeling factor is involved in cell growth arrest, apoptosis and senescence of rat mesenchymal stem cells. J. Cell Sci. 120 (2007) 2904-2911
162. Nie Z., Xue Y., Yang D., Zhou S., Deroo B.J., Archer T.K., et al. A specificity and targeting subunit of a human SWI/SNF family-related chromatin-remodeling complex. Mol. Cell. Biol. 20 (2000) 8879-8888
163. Noh Y.S., and Amasino R.M. PIE1, an ISWI family gene, is required for FLC activation and floral repression in Arabidopsis. Plant Cell 15 (2003) 1671-1682
164. O'Dor E., Beck S.A., and Brock H.W. Polycomb group mutants exhibit mitotic defects in syncytial cell cycles of Drosophila embryos. Dev. Biol. 290 (2006) 312-322
165. Ogiwara H., Enomoto T., and Seki M. The INO80 chromatin remodeling complex functions in sister chromatid cohesion. Cell Cycle 6 (2007) 1090-1095
166. Ogiwara H., Ui A., Kawashima S., Kugou K., Onoda F., Iwahashi H., et al. Actin-related protein Arp4 functions in kinetochore assembly. Nucleic Acids Res. 35 (2007) 3109-3117
167. Ohfuchi E., Nishimori K., and Harata M. Alternative splicing products of the gene for a human nuclear actin-related protein, hArpNbeta/Baf53, that encode a protein isoform, hArpNbetaS, in the cytoplasm. Biosci. Biotechnol. Biochem. 66 (2002) 1740-1743
168. Ohfuchi E., Kato M., Sasaki M., Sugimoto K., Oma Y., and Harata M. Vertebrate Arp6, a novel nuclear actin-related protein, interacts with heterochromatin protein 1. Eur. J. Cell Biol. 85 (2006) 411-421
169. Okazaki N., Ikeda S., Ohara R., Shimada K., Yanagawa T., Nagase T., et al. The novel protein complex with SMARCAD1/KIAA1122 binds to the vicinity of TSS. J. Mol. Biol. 382 (2008) 257-265
170. 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
171. Olave I.A., Reck-Peterson S.L., and Crabtree G.R. Nuclear actin and actin-related proteins in chromatin remodeling. Annu. Rev. Biochem. 71 (2002) 755-781
172. Oma Y., Nishimori K., and Harata M. The brain-specific actin-related protein ArpN alpha interacts with the transcriptional co-repressor CtBP. Biochem. Biophys. Res. Commun. 301 (2003) 521-528
173. Ooi S.L., and Henikoff S. Germline histone dynamics and epigenetics. Curr. Opin. Cell Biol. 19 (2007) 257-265
174. Osley M.A., Tsukuda T., and Nickoloff J.A. ATP-dependent chromatin remodeling factors and DNA damage repair. Mutat. Res. 618 (2007) 65-80
175. Papoulas O., Beek S.J., Moseley S.L., McCallum C.M., Sarte M., Shearn A., et al. The Drosophila trithorax group proteins BRM, ASH1 and ASH2 are subunits of distinct protein complexes. Development 125 (1998) 3955-3966
176. Park J., Wood M.A., and Cole M.D. BAF53 forms distinct nuclear complexes and functions as a critical c-Myc-interacting nuclear cofactor for oncogenic transformation. Mol. Cell. Biol. 22 (2002) 1307-1316
177. Park J.H., Park E.J., Lee H.S., Kim S.J., Hur S.K., Imbalzano A.N., et al. Mammalian SWI/SNF complexes facilitate DNA double-strand break repair by promoting gamma-H2AX induction. Embo J. 25 (2006) 3986-3997
178. Park J.H., Park E.J., Hur S.K., Kim S., and Kwon J. Mammalian SWI/SNF chromatin remodeling complexes are required to prevent apoptosis after DNA damage. DNA Repair (Amst) 8 (2009) 29-39
179. Peterson C.L., Zhao Y., and Chait B.T. Subunits of the yeast SWI/SNF complex are members of the actin-related protein (ARP) family. J. Biol. Chem. 273 (1998) 23641-23644
180. Pien S., Fleury D., Mylne J.S., Crevillen P., Inze D., Avramova Z., et al. ARABIDOPSIS TRITHORAX1 dynamically regulates FLOWERING LOCUS C activation via histone 3 lysine 4 trimethylation. Plant Cell 20 (2008) 580-588
181. Pillus L., and Rine J. Epigenetic inheritance of transcriptional states in S. cerevisiae. Cell 59 (1989) 637-647
182. Poch O., and Winsor B. Who's who among the Saccharomyces cerevisiae actin-related proteins? A classification and nomenclature proposal for a large family. Yeast 13 (1997) 1053-1058
183. Putterill J., Robson F., Lee K., Simon R., and Coupland G. The CONSTANS gene of Arabidopsis promotes flowering and encodes a protein showing similarities to zinc finger transcription factors. Cell 80 (1995) 847-857
184. Putterill J., Laurie R., and Macknight R. It's time to flower: the genetic control of flowering time. Bioessays 26 (2004) 363-373
185. Raisner R.M., and Madhani H.D. Patterning chromatin: form and function for H2A.Z variant nucleosomes. Curr. Opin. Genet. Dev. 16 (2006) 119-124
186. Raisner R.M., Hartley P.D., Meneghini M.D., Bao M.Z., Liu C.L., Schreiber S.L., et al. Histone variant H2A.Z marks the 5′ ends of both active and inactive genes in euchromatin. Cell 123 (2005) 233-248
187. Rando O.J., Zhao K., Janmey P., and Crabtree G.R. Phosphatidylinositol-dependent actin filament binding by the SWI/SNF-like BAF chromatin remodeling complex. Proc. Natl. Acad. Sci. USA 99 (2002) 2824-2829
188. Remus R., Kanzaki A., Yawata A., Nakanishi H., Wada H., Sugihara T., et al. DNA methylation in promoter regions of red cell membrane protein genes in healthy individuals and patients with hereditary membrane disorders. Int. J. Hematol. 81 (2005) 385-395
189. Roberts J.A. Abscission and dehiscence. Symp. Soc. Exp. Biol. 52 (2000) 203-211
190. Robertson K.D., and Wolffe A.P. DNA methylation in health and disease. Nat. Rev. Genet. 1 (2000) 11-19
191. Rogers H.J. Programmed cell death in floral organs: how and why do flowers die?. Ann. Bot. (Lond) 97 (2006) 309-315
192. Roux-Rouquie M. Genetic and epigenetic regulation schemes: need for an alternative paradigm. Mol. Genet. Metab. 71 (2000) 1-9
193. Ruhl D.D., Jin J., Cai Y., Swanson S., Florens L., Washburn M.P., et al. Purification of a human SRCAP complex that remodels chromatin by incorporating the histone variant H2A.Z into nucleosomes. Biochemistry 45 (2006) 5671-5677
194. Samach A., Onouchi H., Gold S.E., Ditta G.S., Schwarz-Sommer Z., Yanofsky M.F., et al. Distinct roles of CONSTANS target genes in reproductive development of Arabidopsis. Science 288 (2000) 1613-1616
195. Samuelson A.V., Narita M., Chan H.M., Jin J., de Stanchina E., McCurrach M.E., et al. p400 is required for E1A to promote apoptosis. J. Biol. Chem. 280 (2005) 21915-21923
196. Sansam C.G., and Roberts C.W. Epigenetics and cancer: altered chromatin remodeling via Snf5 loss leads to aberrant cell cycle regulation. Cell Cycle 5 (2006) 621-624
197. Santisteban M.S., Kalashnikova T., and Smith M.M. Histone H2A.Z regulates transcription and is partially redundant with nucleosome remodeling complexes. Cell 103 (2000) 411-422
198. Sardiu M.E., Cai Y., Jin J., Swanson S.K., Conaway R.C., Conaway J.W., et al. Probabilistic assembly of human protein interaction networks from label-free quantitative proteomics. Proc. Natl. Acad. Sci. USA 105 (2008) 1454-1459
199. Sarnowski T.J., Rios G., Jasik J., Swiezewski S., Kaczanowski S., Li Y., et al. SWI3 subunits of putative SWI/SNF chromatin-remodeling complexes play distinct roles during Arabidopsis development. Plant Cell 17 (2005) 2454-2472
200. Saze H., Sasaki T., and Kakutani T. Negative regulation of DNA methylation in plants. Epigenetics 3 (2008) 122-124
201. Schulz W.A., Steinhoff C., and Florl A.R. Methylation of endogenous human retroelements in health and disease. Curr. Top. Microbiol. Immunol. 310 (2006) 211-250
202. Seah C., Levy M.A., Jiang Y., Mokhtarzada S., Higgs D.R., Gibbons R.J., et al. Neuronal death resulting from targeted disruption of the Snf2 protein ATRX is mediated by p53. J. Neurosci. 28 (2008) 12570-12580
203. Shaked H., Avivi-Ragolsky N., and Levy A.A. Involvement of the Arabidopsis SWI2/SNF2 chromatin remodeling gene family in DNA damage response and recombination. Genetics 173 (2006) 985-994
204. Shames D.S., Minna J.D., and Gazdar A.F. DNA methylation in health, disease, and cancer. Curr. Mol. Med. 7 (2007) 85-102
205. Shanahan F., Seghezzi W., Parry D., Mahony D., and Lees E. Cyclin E associates with BAF155 and BRG1, components of the mammalian SWI-SNF complex, and alters the ability of BRG1 to induce growth arrest. Mol. Cell. Biol. 19 (1999) 1460-1469
206. Shen X., Mizuguchi G., Hamiche A., and Wu C. A chromatin remodelling complex involved in transcription and DNA processing. Nature 406 (2000) 541-544
207. Shen J., Hsu C.M., Kang B.K., Rosen B.P., and Bhattacharjee H. The Saccharomyces cerevisiae Arr4p is involved in metal and heat tolerance. Biometals 16 (2003) 369-378
208. Shen X., Ranallo R., Choi E., and Wu C. Involvement of actin-related proteins in ATP-dependent chromatin remodeling. Mol. Cell 12 (2003) 147-155
209. Shimada K., Oma Y., Schleker T., Kugou K., Ohta K., Harata M., et al. Ino80 chromatin remodeling complex promotes recovery of stalled replication forks. Curr. Biol. 18 (2008) 566-575
210. 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
211. Simpson G.G. The autonomous pathway: epigenetic and post-transcriptional gene regulation in the control of Arabidopsis flowering time. Curr. Opin. Plant Biol. 7 (2004) 570-574
212. Simpson G.G., and Dean C. Arabidopsis, the Rosetta stone of flowering time?. Science 296 (2002) 285-289
213. Smerdon M.J., and Lieberman M.W. Nucleosome rearrangement in human chromatin during UV-induced DNA- reapir synthesis. Proc. Natl. Acad. Sci. USA 75 (1978) 4238-4241
214. Smith H.S., Springer E.L., and Hackett A.J. Nuclear ultrastructure of epithelial cell lines derived from human carcinomas and nonmalignant tissues. Cancer Res. 39 (1979) 332-344
215. Soragni E., Herman D., Dent S.Y., Gottesfeld J.M., Wells R.D., and Napierala M. Long intronic GAATTC repeats induce epigenetic changes and reporter gene silencing in a molecular model of Friedreich ataxia. Nucleic Acids Res. 36 (2008) 6056-6065
216. Staehling-Hampton K., Ciampa P.J., Brook A., and Dyson N. A genetic screen for modifiers of E2F in Drosophila melanogaster. Genetics 153 (1999) 275-287
217. Stefanov S.A. Further characterization of the actin-related protein Act3p/Arp4 of S. cerevisiae through mutational analysis. Mol. Biol. Rep. 27 (2000) 35-43
218. Steinboeck F., Krupanska L., Bogusch A., Kaufmann A., and Heidenreich E. Novel regulatory properties of Saccharomyces cerevisiae Arp4. J. Biochem. (Tokyo) 139 (2006) 741-751
219. Su Y., Kwon C.S., Bezhani S., Huvermann B., Chen C., Peragine A., et al. The N-terminal ATPase AT-hook-containing region of the Arabidopsis chromatin-remodeling protein SPLAYED is sufficient for biological activity. Plant J. 46 (2006) 685-699
220. Sumi-Ichinose C., Ichinose H., Metzger D., and Chambon P. SNF2beta-BRG1 is essential for the viability of F9 murine embryonal carcinoma cells. Mol. Cell. Biol. 17 (1997) 5976-5986
221. Sunada R., Gorzer I., Oma Y., Yoshida T., Suka N., Wintersberger U., et al. The nuclear actin-related protein Act3p/Arp4p is involved in the dynamics of chromatin-modulating complexes. Yeast 22 (2005) 753-768
222. Szerlong H., Saha A., and Cairns B.R. The nuclear actin-related proteins Arp7 and Arp9: a dimeric module that cooperates with architectural proteins for chromatin remodeling. EMBO J. 22 (2003) 3175-3187
223. Szerlong H., Hinata K., Viswanathan R., Erdjument-Bromage H., Tempst P., and Cairns B.R. The HSA domain binds nuclear actin-related proteins to regulate chromatin-remodeling ATPases. Nat. Struct. Mol. Biol. 15 (2008) 469-476
224. Tamura K., Dudley J., Nei M., and Kumar S. MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol. Biol. Evol. 24 (2007) 1596-1599
225. Tromans A. Cardiovascular biology: how genes know their place. Nature 432 (2004) 29
226. True H.L., Berlin I., and Lindquist S.L. Epigenetic regulation of translation reveals hidden genetic variation to produce complex traits. Nature 431 (2004) 184-187
227. Trujillo K.M., and Osley M.A. INO80 meets a fork in the road. Nat. Struct. Mol. Biol. 15 (2008) 332-334
228. Ueno M., Murase T., Kibe T., Ohashi N., Tomita K., Murakami Y., et al. Fission yeast Arp6 is required for telomere silencing, but functions independently of Swi6. Nucleic Acids Res. 32 (2004) 736-741
229. 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
230. van Attikum H., Fritsch O., and Gasser S.M. Distinct roles for SWR1 and INO80 chromatin remodeling complexes at chromosomal double-strand breaks. EMBO J. 26 (2007) 4113-4125
231. van den Ent F., Amos L., and Lowe J. Prokaryotic origin of the actin cytoskeleton. Nature 413 (2001) 39-44
232. Vasanthi D., and Mishra R.K. Epigenetic regulation of genes during development: a conserved theme from flies to mammals. J. Genet. Genomics 35 (2008) 413-429
233. Vignon X., Zhou Q., and Renard J.P. Chromatin as a regulative architecture of the early developmental functions of mammalian embryos after fertilization or nuclear transfer. Cloning Stem Cells 4 (2002) 363-377
234. Voitenko V.P. Aging, diseases and X-chromatin. Z. Gerontol. 13 (1980) 18-23
235. Waddington C.H. The strategy of the genes. The Strategy of the Genes (1995), George Allen & Unwin Ltd, London, Ruskin House 257
236. Wagner D., and Meyerowitz E.M. SPLAYED, a novel SWI/SNF ATPase homolog, controls reproductive development in Arabidopsis. Curr. Biol. 12 (2002) 85-94
237. Walley J.W., Rowe H.C., Xiao Y., Chehab E.W., Kliebenstein D.J., Wagner D., et al. The chromatin remodeler SPLAYED regulates specific stress signaling pathways. PLoS Pathog. 4 (2008) e1000237
238. Wang W., Cote J., Xue Y., Zhou S., Khavari P.A., Biggar S.R., et al. Purification and biochemical heterogeneity of the mammalian SWI-SNF complex. EMBO J. 15 (1996) 5370-5382
239. Wang W., Xue Y., Zhou S., Kuo A., Cairns B.R., and Crabtree G.R. Diversity and specialization of mammalian SWI/SNF complexes. Genes Dev. 10 (1996) 2117-2130
240. Wang M., Gu C., Qi T., Tang W., Wang L., Wang S., et al. BAF53 interacts with p53 and functions in p53-mediated p21-gene transcription. J. Biochem. 142 (2007) 613-620
241. Weber V., Harata M., Hauser H., and Wintersberger U. The actin-related protein Act3p of Saccharomyces cerevisiae is located in the nucleus. Mol. Biol. Cell 6 (1995) 1263-1270
242. Weinhold B. Epigenetics: the science of change. Environ. Health Perspect. 114 (2006) A160-A167
243. Williams L., and Fletcher J.C. Stem cell regulation in the Arabidopsis shoot apical meristem. Curr. Opin. Plant Biol. 8 (2005) 582-586
244. Wilson A.C., and Sarich V.M. A molecular time scale for human evolution. Proc. Natl. Acad. Sci. USA 63 (1969) 1088-1093
245. Wong J.J., Hawkins N.J., and Ward R.L. Colorectal cancer: a model for epigenetic tumorigenesis. Gut 56 (2007) 140-148
246. Wu W.H., Alami S., Luk E., Wu C.H., Sen S., Mizuguchi G., et al. Swc2 is a widely conserved H2AZ-binding module essential for ATP-dependent histone exchange. Nat. Struct. Mol. Biol. 12 (2005) 1064-1071
247. Wu J.I., Lessard J., Olave I.A., Qiu Z., Ghosh A., Graef I.A., et al. Regulation of dendritic development by neuron-specific chromatin remodeling complexes. Neuron 56 (2007) 94-108
248. Wu K., Zhang L., Zhou C., Yu C.W., and Chaikam V. HDA6 is required for jasmonate response, senescence and flowering in Arabidopsis. J. Exp. Bot. 59 (2008) 225-234
249. Yang X., Zaurin R., Beato M., and Peterson C.L. Swi3p controls SWI/SNF assembly and ATP-dependent H2A-H2B displacement. Nat. Struct. Mol. Biol. 14 (2007) 540-547
250. Yeh J.H., Spicuglia S., Kumar S., Sanchez-Sevilla A., Ferrier P., and Imbert J. Control of IL-2Ralpha gene expression: structural changes within the proximal enhancer/core promoter during T-cell development. Nucleic Acids Res. 30 (2002) 1944-1951
251. Young D.W., Pratap J., Javed A., Weiner B., Ohkawa Y., van Wijnen A., et al. 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
252. Yuan G.C., Liu Y.J., Dion M.F., Slack M.D., Wu L.F., Altschuler S.J., et al. Genome-scale identification of nucleosome positions in S. cerevisiae. Science 309 (2005) 626-630
253. Zeisig B.B., Cheung N., Yeung J., and So C.W. Reconstructing the disease model and epigenetic networks for MLL-AF4 leukemia. Cancer Cell 14 (2008) 345-347
254. Zhang H.S., Gavin M., Dahiya A., Postigo A.A., Ma D., Luo R.X., et al. Exit from G1 and S phase of the cell cycle is regulated by repressor complexes containing HDAC-Rb-hSWI/SNF and Rb-hSWI/SNF. Cell 101 (2000) 79-89
255. Zhang J., Wang L., Zhuang L., Huo L., Musa S., Li S., et al. Arp11 affects dynein-dynactin interaction and is essential for dynein function in Aspergillus nidulans. Traffic 9 (2008) 1073-1087
256. Zhao K., Wang W., Rando O.J., Xue Y., Swiderek K., Kuo A., et al. Rapid and phosphoinositol-dependent binding of the SWI/SNF-like BAF complex to chromatin after T lymphocyte receptor signaling. Cell 95 (1998) 625-636
257. Zhou C., Miki B., and Wu K. CHB2, a member of the SWI3 gene family, is a global regulator in Arabidopsis. Plant Mol. Biol. 52 (2003) 1125-1134