Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivo (original) (raw)
Kornberg, R.D. Structure of chromatin. Annu. Rev. Biochem.46, 931–954 (1977). ArticleCAS Google Scholar
Yuan, G.-C. et al. Genome-scale identification of nucleosome positions in S. cerevisiae. Science309, 626–630 (2005). ArticleCAS Google Scholar
Lee, W. et al. A high-resolution atlas of nucleosome occupancy in yeast. Nat. Genet.39, 1235–1244 (2007). ArticleCAS Google Scholar
Mavrich, T.N. et al. Nucleosome organization in the Drosophila genome. Nature453, 358–362 (2008). ArticleCAS Google Scholar
Schones, D.E. et al. Dynamic regulation of nucleosome positioning in the human genome. Cell132, 887–898 (2008). ArticleCAS Google Scholar
Shivaswamy, S. et al. Dynamic remodeling of individual nucleosomes across a eukaryotic genome in response to transcriptional perturbation. PLoS Biol.6, e65 (2008). Article Google Scholar
Valouev, A. et al. A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning. Genome Res.18, 1051–1063 (2008). ArticleCAS Google Scholar
Mavrich, T.N. et al. A barrier nucleosome model for statistical positioning of nucleosome throughout the yeast genome. Genome Res.18, 1073–1083 (2008). ArticleCAS Google Scholar
Deckert, J. & Struhl, K. Histone acetylation at promoters is differentially affected by activators and repressors. Mol. Cell. Biol.21, 2726–2735 (2001). ArticleCAS Google Scholar
Boeger, H. et al. Nucleosomes unfold completely at a transcriptionally active promoter. Mol. Cell11, 1587–1598 (2003). ArticleCAS Google Scholar
Reinke, H. & Horz, W. Histones are first hyperacetylated and then lose contact with the activated PHO5 promoter. Mol. Cell11, 1599–1607 (2003). ArticleCAS Google Scholar
Schwabish, M.A. & Struhl, K. The Swi/Snf complex is important for histone eviction during transcriptional activation and RNA polymerase II elongation in vivo. Mol. Cell. Biol.27, 6987–6995 (2007). ArticleCAS Google Scholar
Kristjuhan, A. & Svejstrup, J.Q. Evidence for distinct mechanisms facilitating transcript elongation through chromatin in vivo. EMBO J.23, 4243–4252 (2004). ArticleCAS Google Scholar
Lee, C.K. et al. Evidence for nucleosome depletion at active regulatory regions genome-wide. Nat. Genet.36, 900–905 (2004). ArticleCAS Google Scholar
Schwabish, M.A. & Struhl, K. Evidence for eviction and rapid deposition of histones upon transcriptional elongation by RNA polymerase II. Mol. Cell. Biol.24, 10111–10117 (2004). ArticleCAS Google Scholar
Kaplan, N. et al. The DNA-encoded nucleosome organization of a eukaryotic genome. Nature458, 362–366 (2009). ArticleCAS Google Scholar
Sekinger, E.A., Moqtaderi, Z. & Struhl, K. Intrinsic histone-DNA interactions and low nucleosome density are important for preferential accessibility of promoter regions in yeast. Mol. Cell18, 735–748 (2005). ArticleCAS Google Scholar
Iyer, V. & Struhl, K. Poly(dA:dT), a ubiquitous promoter element that stimulates transcription via its intrinsic structure. EMBO J.14, 2570–2579 (1995). ArticleCAS Google Scholar
Drew, H.R. & Travers, A.A. DNA bending and its relation to nucleosome positioning. J. Mol. Biol.186, 773–790 (1985). ArticleCAS Google Scholar
Satchwell, S.C., Drew, H.R. & Travers, A.A. Sequence periodicities in chicken nucleosome core DNA. J. Mol. Biol.191, 659–675 (1986). ArticleCAS Google Scholar
Widom, J. Role of DNA sequence in nucleosome stability and dynamics. Q. Rev. Biophys.34, 269–324 (2001). ArticleCAS Google Scholar
Fedor, M.J., Lue, N.F. & Kornberg, R.D. Statistical positioning of nucleosomes by specific protein binding to an upstream activating sequence in yeast. J. Mol. Biol.204, 109–127 (1988). ArticleCAS Google Scholar
Lowary, P.T. & Widom, J. New DNA sequence rules for high affinity binding to histone octamer and sequence-directed nucleosome positioning. J. Mol. Biol.276, 19–42 (1998). ArticleCAS Google Scholar
Segal, E. et al. A genomic code for nucleosome positioning. Nature442, 772–778 (2006). ArticleCAS Google Scholar
Whitehouse, I. & Tsukiyama, T. Antagonistic forces that position nucleosomes in vivo. Nat. Struct. Mol. Biol.13, 633–640 (2006). ArticleCAS Google Scholar
Yang, A. et al. Relationships between p63 binding, DNA sequence, transcription activity, and biological function in human cells. Mol. Cell24, 593–602 (2006). ArticleCAS Google Scholar
Liu, X. et al. Whole-genome comparison of Leu3 binding in vitro and in vivo reveals the importance of nucleosome occupancy in target site selection. Genome Res.16, 1517–1528 (2006). ArticleCAS Google Scholar
Hörz, W. & Altenburger, W. Sequence specific cleavage of DNA by micrococcal nuclease. Nucleic Acids Res.9, 2643–2658 (1981). Article Google Scholar
Struhl, K. Yeast transcriptional regulatory mechanisms. Annu. Rev. Genet.29, 651–674 (1995). ArticleCAS Google Scholar
Muse, G.W. et al. RNA polymerase is poised for activation across the genome. Nat. Genet.39, 1507–1511 (2007). ArticleCAS Google Scholar
Steinmetz, E.J. et al. Genome-wide distribution of yeast RNA polymerase II and its control by Sen1 helicase. Mol. Cell24, 735–746 (2006). ArticleCAS Google Scholar
Struhl, K. Transcriptional noise and the fidelity of initiation by RNA polymerase II. Nat. Struct. Mol. Biol.14, 103–105 (2007). ArticleCAS Google Scholar
Dion, M.F. et al. Dynamics of replication-independent histone turnover in budding yeast. Science315, 1405–1408 (2007). ArticleCAS Google Scholar
Fyodorov, D.V. & Kadonaga, J.T. Chromatin assembly in vitro with purified recombinant ACF and NAP-1. Methods Enzymol.371, 499–515 (2003). ArticleCAS Google Scholar