Dynamic chromatin: concerted nucleosome remodelling and acetylation

References

Bourachot, B., Yaniv, M., and Muchardt, C. (2003). Growth inhibition by the mammalian SWI-SNF subunit Brm is regulated by acetylation. EMBO J.22, 6505–6515.10.1093/emboj/cdg621Suche in Google Scholar

Bowen, N.J., Fujita, N., Kajita, M., and Wade, P.A. (2004). Mi-2/NuRD: multiple complexes for many purposes. Biochim. Biophys. Acta1677, 52–57.10.1016/j.bbaexp.2003.10.010Suche in Google Scholar

Brooks, C.L. and Gu, W. (2003). Ubiquitination, phosphorylation and acetylation: the molecular basis for p53 regulation. Curr. Opin. Cell Biol.15, 164–171.10.1016/S0955-0674(03)00003-6Suche in Google Scholar

Cho, K.S., Elizondo, L.I., and Boerkoel, C.F. (2004). Advances in chromatin remodeling and human disease. Curr. Opin. Genet. Dev.14, 308–315.10.1016/j.gde.2004.04.015Suche in Google Scholar PubMed

Clapier, C.R., Nightingale, K.P., and Becker, P.B. (2002). A critical epitope for substrate recognition by the nucleosome remodeling ATPase ISWI. Nucleic Acids Res.30, 649–655.10.1093/nar/30.3.649Suche in Google Scholar PubMed PubMed Central

Corona, D.F., Clapier, C.R., Becker, P.B., and Tamkun, J.W. (2002). Modulation of ISWI function by site-specific histone acetylation. EMBO Rep.3, 242–247.10.1093/embo-reports/kvf056Suche in Google Scholar PubMed PubMed Central

de la Cruz, X., Lois, S., Sanchez-Molina, S., and Martinez-Balbas, M.A. (2005). Do protein motifs read the histone code? Bioessays27, 164–175.10.1002/bies.20176Suche in Google Scholar PubMed

De La Fuente, R., Viveiros, M.M., Wigglesworth, K., and Eppig, J.J. (2004). ATRX, a member of the SNF2 family of helicase/ATPases, is required for chromosome alignment and meiotic spindle organization in metaphase II stage mouse oocytes. Dev. Biol.272, 1–14.Suche in Google Scholar

Dhasarathy, A. and Kladde, M.P. (2005). Promoter occupancy is a major determinant of chromatin remodeling enzyme requirements. Mol. Cell. Biol.25, 2698–2707.10.1128/MCB.25.7.2698-2707.2005Suche in Google Scholar PubMed PubMed Central

Downs, J.A. and Jackson, S.P. (2004). A means to a DNA end: the many roles of Ku. Nat. Rev. Mol. Cell Biol.5, 367–378.10.1038/nrm1367Suche in Google Scholar PubMed

Eberharter, A. and Becker, P.B. (2002). Histone acetylation: a switch between repressive and permissive chromatin. Second in review series on chromatin dynamics. EMBO Rep.3, 224–229.10.1093/embo-reports/kvf053Suche in Google Scholar PubMed PubMed Central

Eberharter, A. and Becker, P.B. (2004). ATP-dependent nucleosome remodelling: factors and functions. J. Cell Sci.117, 3707–3711.10.1242/jcs.01175Suche in Google Scholar

Feng, Q. and Zhang, Y. (2003). The NuRD complex: linking histone modification to nucleosome remodeling. Curr. Top. Microbiol. Immunol.274, 269–290.10.1007/978-3-642-55747-7_10Suche in Google Scholar

Grummt, I. and Pikaard, C.S. (2003). Epigenetic silencing of RNA polymerase I transcription. Nat. Rev. Mol. Cell Biol.4, 641–649.10.1038/nrm1171Suche in Google Scholar

Gunawardena, R.W., Siddiqui, H., Solomon, D.A., Mayhew, C.N., Held, J., Angus, S.P., and Knudsen, E.S. (2004). Hierarchical requirement of SWI/SNF in retinoblastoma tumor suppressor-mediated repression of Plk1. J. Biol. Chem.279, 29278–29285.10.1074/jbc.M400395200Suche in Google Scholar

Hassan, A.H., Prochasson, P., Neely, K.E., Galasinski, S.C., Chandy, M., Carrozza, M.J., and Workman, J.L. (2002). Function and selectivity of bromodomains in anchoring chromatin-modifying complexes to promoter nucleosomes. Cell111, 369–379.10.1016/S0092-8674(02)01005-XSuche in Google Scholar

Huang, Z.Q., Li, J., Sachs, L.M., Cole, P.A., and Wong, J. (2003). A role for cofactor–cofactor and cofactor–histone interactions in targeting p300, SWI/SNF and Mediator for transcription. EMBO J.22, 2146–2155.10.1093/emboj/cdg219Suche in Google Scholar

Kanno, T., Kanno, Y., Siegel, R.M., Jang, M.K., Lenardo, M.J., and Ozato, K. (2004). Selective recognition of acetylated histones by bromodomain proteins visualized in living cells. Mol. Cell13, 33–43.10.1016/S1097-2765(03)00482-9Suche in Google Scholar

Kasten, M., Szerlong, H., Erdjument-Bromage, H., Tempst, P., Werner, M., and Cairns, B.R. (2004). Tandem bromodomains in the chromatin remodeler RSC recognize acetylated histone H3 Lys14. EMBO J.23, 1348–1359.10.1038/sj.emboj.7600143Suche in Google Scholar

Krogan, N.J., Keogh, M.C., Datta, N., Sawa, C., Ryan, O.W., Ding, H., Haw, R.A., Pootoolal, J., Tong, A., Canadien, V., et al. (2003). A Snf2 family ATPase complex required for recruitment of the histone H2A variant Htz1. Mol. Cell12, 1565–1576.10.1016/S1097-2765(03)00497-0Suche in Google Scholar

Kusch, T., Florens, L., Macdonald, W.H., Swanson, S.K., Glaser, R.L., Yates, J.R. 3^rd, Abmayr, S.M., Washburn, M.P., and Workman, J.L. (2004). Acetylation by Tip60 is required for selective histone variant exchange at DNA lesions. Science306, 2084–2087.10.1126/science.1103455Suche in Google Scholar PubMed

Ladurner, A.G., Inouye, C., Jain, R., and Tjian, R. (2003). Bromodomains mediate an acetyl-histone encoded antisilencing function at heterochromatin boundaries. Mol. Cell11, 365–376.10.1016/S1097-2765(03)00035-2Suche in Google Scholar

Längst, G. and Becker, P.B. (2004). Nucleosome remodeling: one mechanism, many phenomena? Biochim. Biophys. Acta1677, 58–63.10.1016/j.bbaexp.2003.10.011Suche in Google Scholar

Lemieux, K. and Gaudreau, L. (2004). Targeting of Swi/Snf to the yeast GAL1 UAS G requires the Mediator, TAF IIs, and RNA polymerase II. EMBO J.23, 4040–4050.10.1038/sj.emboj.7600416Suche in Google Scholar

Matangkasombut, O. and Buratowski, S. (2003). Different sensitivities of bromodomain factors 1 and 2 to histone H4 acetylation. Mol. Cell11, 353–363.10.1016/S1097-2765(03)00033-9Suche in Google Scholar

Mellor, J. and Morillon, A. (2004). ISWI complexes in Saccharomyces cerevisiae. Biochim. Biophys. Acta1677, 100–112.10.1016/j.bbaexp.2003.10.014Suche in Google Scholar

Memedula, S. and Belmont, A.S. (2003). Sequential recruitment of HAT and SWI/SNF components to condensed chromatin by VP16. Curr. Biol.13, 241–246.10.1016/S0960-9822(03)00048-4Suche in Google Scholar

Metivier, R., Penot, G., Hubner, M.R., Reid, G., Brand, H., Kos, M., and Gannon, F. (2003). Estrogen receptor α directs ordered, cyclical, and combinatorial recruitment of cofactors on a natural target promoter. Cell115, 751–763.10.1016/S0092-8674(03)00934-6Suche in Google Scholar

Morrison, A.J., Highland, J., Krogan, N.J., Arbel-Eden, A., Greenblatt, J.F., Haber, J.E., and Shen, X. (2004). INO80 and γ-H2AX interaction links ATP-dependent chromatin remodeling to DNA damage repair. Cell119, 767–775.10.1016/j.cell.2004.11.037Suche in Google Scholar

Nagaich, A.K., Walker, D.A., Wolford, R., and Hager, G.L. (2004). Rapid periodic binding and displacement of the glucocorticoid receptor during chromatin remodeling. Mol. Cell14, 163–174.10.1016/S1097-2765(04)00178-9Suche in Google Scholar

Narlikar, G.J., Fan, H.Y., and Kingston, R.E. (2002). Cooperation between complexes that regulate chromatin structure and transcription. Cell108, 475–487.10.1016/S0092-8674(02)00654-2Suche in Google Scholar

Neely, K.E. and Workman, J.L. (2002). Histone acetylation and chromatin remodeling: which comes first? Mol. Genet. Metab.76, 1–5.10.1016/S1096-7192(02)00014-8Suche in Google Scholar

Nourani, A., Utley, R.T., Allard, S., and Cote, J. (2004). Recruitment of the NuA4 complex poises the PHO5 promoterfor chromatin remodeling and activation. EMBO J.23, 2597–2607.10.1038/sj.emboj.7600230Suche in Google Scholar

Peterson, C.L. and Cote, J. (2004). Cellular machineries for chromosomal DNA repair. Genes Dev.18, 602–616.10.1101/gad.1182704Suche in Google Scholar

Pray-Grant, M.G., Daniel, J.A., Schieltz, D., Yates, J.R. 3^rd, and Grant, P.A. (2005). Chd1 chromodomain links histone H3 methylation with SAGA- and SLIK-dependent acetylation. Nature433, 434–438.10.1038/nature03242Suche in Google Scholar

Reinke, H. and Horz, W. (2003). Histones are first hyperacetylated and then lose contact with the activated PHO5 promoter. Mol. Cell11, 1599–1607.10.1016/S1097-2765(03)00186-2Suche in Google Scholar

Roth, S.Y., Denu, J.M., and Allis, C.D. (2001). Histone acetyltransferases. Annu. Rev. Biochem.70, 81–120.10.1146/annurev.biochem.70.1.81Suche in Google Scholar PubMed

Santoro, R. and 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, 2539–2546.10.1128/MCB.25.7.2539-2546.2005Suche in Google Scholar PubMed PubMed Central

Santoro, R., Li, J., and Grummt, I. (2002). The nucleolar remodeling complex NoRC mediates heterochromatin formation and silencing of ribosomal gene transcription. Nat. Genet.32, 393–396.10.1038/ng1010Suche in Google Scholar PubMed

Sif, S. (2004). ATP-dependent nucleosome remodeling complexes: enzymes tailored to deal with chromatin. J. Cell. Biochem.91, 1087–1098.10.1002/jcb.20005Suche in Google Scholar PubMed

Simic, R., Lindstrom, D.L., Tran, H.G., Roinick, K.L., Costa, P.J., Johnson, A.D., Hartzog, G.A., and Arndt, K.M. (2003). Chromatin remodeling protein Chd1 interacts with transcription elongation factors and localizes to transcribed genes. EMBO J.22, 1846–1856.10.1093/emboj/cdg179Suche in Google Scholar PubMed PubMed Central

Soutoglou, E. and Talianidis, I. (2002). Coordination of PIC assembly and chromatin remodeling during differentiation-induced gene activation. Science295, 1901–1904.10.1126/science.1068356Suche in Google Scholar

Steger, D.J., Haswell, E.S., Miller, A.L., Wente, S.R., and O'Shea, E.K. (2003). Regulation of chromatin remodeling by inositol polyphosphates. Science299, 114–116.10.1126/science.1078062Suche in Google Scholar

Turner, B.M. (2005). Reading signals on the nucleosome with a new nomenclature for modified histones. Nat. Struct. Mol. Biol.12, 110–112.10.1038/nsmb0205-110Suche in Google Scholar

Vaquero, A., Loyola, A., and Reinberg, D. (2003). The constantly changing face of chromatin. Sci. Aging Knowledge Environ. RE4.Suche in Google Scholar

Wang, W. (2003). The SWI/SNF family of ATP-dependent chromatin remodelers: similar mechanisms for diverse functions. Curr. Top. Microbiol. Immunol.274, 143–169.10.1007/978-3-642-55747-7_6Suche in Google Scholar

Yamada, T., Mizuno, K.I., Hirota, K., Kon, N., Wahls, W.P., Hartsuiker, E., Murofushi, H., Shibata, T., and Ohta, K. (2004). Roles of histone acetylation and chromatin remodeling factor in a meiotic recombination hotspot. EMBO J.23, 1792–1803.10.1038/sj.emboj.7600138Suche in Google Scholar

Yang, X.J. (2004a). The diverse superfamily of lysine acetyltransferases and their roles in leukemia and other diseases. Nucleic Acids Res.32, 959–976.10.1093/nar/gkh252Suche in Google Scholar

Yang, X.J. (2004b). Lysine acetylation and the bromodomain: a new partnership for signaling. Bioessays26, 1076–1087.10.1002/bies.20104Suche in Google Scholar

Zegerman, P., Canas, B., Pappin, D., and Kouzarides, T. (2002). Histone H3 lysine 4 methylation disrupts binding of nucleosome remodeling and deacetylase (NuRD) repressor complex. J. Biol. Chem.277, 11621–11624.10.1074/jbc.C200045200Suche in Google Scholar

Zeng, L. and Zhou, M.M. (2002). Bromodomain: an acetyl-lysine binding domain. FEBS Lett.513, 124–128.10.1016/S0014-5793(01)03309-9Suche in Google Scholar

Zhang, Z. and Reese, J.C. (2004). Ssn6-Tup1 requires the ISW2 complex to position nucleosomes in Saccharomyces cerevisiae. EMBO J.23, 2246–2257.10.1038/sj.emboj.7600227Suche in Google Scholar PubMed PubMed Central

Zhou, J., Chau, C.M., Deng, Z., Shiekhattar, R., Spindler, M.P., Schepers, A., and Lieberman, P.M. (2005). Cell cycle regulation of chromatin at an origin of DNA replication. EMBO J.24, 1406–1417.10.1038/sj.emboj.7600609Suche in Google Scholar PubMed PubMed Central