Determinants of nucleosome organization in primary human cells (original) (raw)
Mellor, J. The dynamics of chromatin remodeling at promoters. Mol. Cell19, 147–157 (2005) ArticleCAS Google Scholar
Radman-Livaja, M. & Rando, O. J. Nucleosome positioning: how is it established, and why does it matter? Dev. Biol.339, 258–266 (2010) ArticleCAS Google Scholar
Kaplan, N. et al. The DNA-encoded nucleosome organization of a eukaryotic genome. Nature458, 362–366 (2009) ArticleADSCAS Google Scholar
Berstein, B. E., Liu, C. L., Humphrey, E. L., Perlstein, E. O. & Schreiber, S. L. Global nucleosome occupancy in yeast. Genome Biol.5, R62 (2004) Article Google Scholar
Yuan, G.-C. et al. Genome-scale identification of nucleosome positions in S.cerevisiae . Science309, 626–630 (2005) ArticleADSCAS Google Scholar
Johnson, S. M., Tan, F. J., McCullough, H. L., Riordan, D. P. & Fire, A. Z. Flexibility and constraint in the nucleosome core landscape of Caenorhabditis elegans chromatin. Genome Res.16, 1505–1516 (2006) ArticleCAS 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
Schones, D. E. et al. Dynamic regulation of nucleosome positioning in the human genome. Cell132, 887–898 (2008) ArticleCAS Google Scholar
Trifonov, E. N. & Sussman, J. L. The pitch of chromatin DNA is reflected in it its nucleotide sequence. Proc. Natl Acad. Sci. USA77, 3816–3820 (1980) ArticleADSCAS Google Scholar
Kornberg, R. D. Structure of chromatin. Ann. Rev. Biochem.46, 931–954 (1977) ArticleCAS Google Scholar
Widom, J. A relationship between the helical twist of DNA and the ordered positioning of nucleosomes in all eukaryotic cells. Proc. Natl Acad. Sci. USA89, 1095–1099 (1992) ArticleADSCAS Google Scholar
Schlegel, R. A., Haye, K. R., Litwack, A. H. & Phelps, B. M. Nucleosome repeat lengths in the definitive erythroid series of the adult chicken. Biochim. Biophys. Acta606, 316–330 (1980) ArticleCAS Google Scholar
Fan, Y. et al. Histone H1 depletion in mammals alters global chromatin structure but causes specific changes in gene regulation. Cell29, 1199–1212 (2005) Article Google Scholar
Mortazavi, A., Williams, B. A., McCue, K., Schaeffer, L. & Wold, B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nature Methods5, 621–628 (2008) ArticleCAS Google Scholar
Valouev, A. et al. Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data. Nature Methods5, 829–834 (2008) ArticleCAS Google Scholar
Barski, A. et al. High-resolution profiling of histone methylations in the human genome. Cell129, 823–837 (2007) ArticleCAS Google Scholar
Wang, Z. et al. Combinatorial patterns of histone acetylations and methylations in the human genome. Nature Genet.40, 897–903 (2008) 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
Segal, E. et al. A genomic code for nucleosome positioning. Nature442, 772–778 (2006) ArticleADSCAS Google Scholar
Hughes, A. & Rando, O. J. Chromatin ‘programming’ by sequence - is there more to the nucleosome code than %GC? J. Biol.8, 96 (2009) Article Google Scholar
Tillo, D. et al. High nucleosome occupancy is encoded at human regulatory sequences. PLoS ONE5, e9129 (2010) ArticleADS Google Scholar
Mavrich, T. N. et al. A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome. Genome Res.18, 1073–1083 (2008) ArticleCAS Google Scholar
Mavrich, T. N. et al. Nucleosome organization in the Drosophila genome. Nature453, 358–362 (2008) ArticleADSCAS Google Scholar
Lee, W. et al. A high-resolution atlas of nucleosome occupancy in yeast. Nature Genet.39, 1235–1244 (2007) ArticleCAS Google Scholar
Gu, S. G. & Fire, A. Partitioning the C.elegans genome by nucleosome modification, occupancy, and positioning. Chromosoma119, 73–87 (2010) ArticleCAS Google Scholar
Sasaki, S. et al. Chromatin-associated periodicity in genetic variation downstream of transcriptional start sites. Science323, 401–404 (2009) ArticleADSCAS Google Scholar
Zhang, Y. et al. Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivo . Nature Struct. Mol. Biol.16, 847–852 (2009) ArticleCAS Google Scholar
Field, Y. et al. Gene expression divergence in yeast is coupled to evolution of DNA-encoded nucleosome organization. Nature Genet.41, 438–445 (2009) ArticleCAS Google Scholar
Chuddapah, S. et al. Global analysis of the insulator binding protein CTCF in chromatin barrier regions reveals demarcation of active and repressive domains. Genome Res.19, 24–32 (2009) Article Google Scholar
Fu, Y., Sinha, M., Peterson, C. L. & Weng, Z. The insulator binding protein CTCF positions 20 nucleosomes around its binding sites across the human genome. PLoS Genet.4, e1000138 (2008) Article Google Scholar
Albert, I. et al. Translational and rotational settings of H2A.Z nucleosomes across the Saccharomyces cerevisiae genome. Nature446, 572–576 (2007) ArticleADSCAS Google Scholar
Wellinger, R. E. & Thoma, F. Nucleosome structure and positioning modulate nucleotide excision repair in the non-transcribed strand of an active gene. EMBO J.16, 5046–5056 (1997) ArticleCAS Google Scholar
Sha, K. et al. Distributed probing of chromatin structure in vivo reveals pervasive chromatin accessibility for expressed and non-expressed genes during tissue differentiation in C.elegans . BMC Genomics11, 465 (2010) Article Google Scholar
Luger, K., Rechsteiner, T. J. & Richmond, T. J. Preparation of nucleosome core particle from recombinant histones. Methods Enzymol.304, 3–19 (1999) ArticleCAS Google Scholar