REFERENCES
- Bannister AJ, et al. 2001. Selective recognition of methylated lysine 9 on histone H3 by the HP1 chromo domain. Nature 410:120–124.
- Bird A, Taggart M, Frommer M, Miller OJ, Macleod D. 1985. A fraction of the mouse genome that is derived from islands of nonmethylated, CpG-rich DNA. Cell 40:91–99.
- Blackledge NP, Klose R. 2011. CpG island chromatin: a platform for gene regulation. Epigenetics 6:147–152.
- Blackledge NP, et al. 2010. CpG islands recruit a histone H3 lysine 36 demethylase. Mol. Cell 38:179–190.
- Capili AD, Schultz DC, Rauscher IF, Borden KL. 2001. Solution structure of the PHD domain from the KAP-1 corepressor: structural determinants for PHD, RING and LIM zinc-binding domains. EMBO J. 20:165–177.
- Carrozza MJ, et al. 2005. Histone H3 methylation by Set2 directs deacetylation of coding regions by Rpd3S to suppress spurious intragenic transcription. Cell 123:581–592.
- Cierpicki T, et al. 2010. Structure of the MLL CXXC domain-DNA complex and its functional role in MLL-AF9 leukemia. Nat. Struct. Mol. Biol. 17:62–68.
- Dhalluin C, et al. 1999. Structure and ligand of a histone acetyltransferase bromodomain. Nature 399:491–496.
- Dyer PN, et al. 2004. Reconstitution of nucleosome core particles from recombinant histones and DNA. Methods Enzymol. 375:23–44.
- Engeholm M, et al. 2009. Nucleosomes can invade DNA territories occupied by their neighbors. Nat. Struct. Mol. Biol. 16:151–158.
- Farnham PJ. 2009. Insights from genomic profiling of transcription factors. Nat. Rev. Genet. 10:605–616.
- Guenther MG, Levine SS, Boyer LA, Jaenisch R, Young RA. 2007. A chromatin landmark and transcription initiation at most promoters in human cells. Cell 130:77–88.
- Guertin MJ, Lis JT. 2010. Chromatin landscape dictates HSF binding to target DNA elements. PLoS Genet. 6:e1001114.
- Hodges C, Bintu L, Lubkowska L, Kashlev M, Bustamante C. 2009. Nucleosomal fluctuations govern the transcription dynamics of RNA polymerase II. Science 325:626–628.
- Izban MG, Luse DS. 1991. Transcription on nucleosomal templates by RNA polymerase II in vitro: inhibition of elongation with enhancement of sequence-specific pausing. Genes Dev. 5:683–696.
- Jeong S, et al. 2009. Selective anchoring of DNA methyltransferases 3A and 3B to nucleosomes containing methylated DNA. Mol. Cell. Biol. 29:5366–5376.
- John S, et al. 2011. Chromatin accessibility pre-determines glucocorticoid receptor binding patterns. Nat. Genet. 43:264–268.
- Johnson DS, Mortazavi A, Myers RM, Wold B. 2007. Genome-wide mapping of in vivo protein-DNA interactions. Science 316:1497–1502.
- Kalkhoven E, Teunissen H, Houweling A, Verrijzer CP, Zantema A. 2002. The PHD type zinc finger is an integral part of the CBP acetyltransferase domain. Mol. Cell. Biol. 22:1961–1970.
- Klose RJ, Bird AP. 2006. Genomic DNA methylation: the mark and its mediators. Trends Biochem. Sci. 31:89–97.
- Kouzarides T. 2007. Chromatin modifications and their function. Cell 128:693–705.
- Lachner M, O'Carroll D, Rea S, Mechtler K, Jenuwein T. 2001. Methylation of histone H3 lysine 9 creates a binding site for HP1 proteins. Nature 410:116–120.
- Li G, et al. 2010. Highly compacted chromatin formed in vitro reflects the dynamics of transcription activation in vivo. Mol. Cell 38:41–53.
- Lidor Nili E, et al. 2010. p53 binds preferentially to genomic regions with high DNA-encoded nucleosome occupancy. Genome Res. 20:1361–1368.
- Lomvardas S, Thanos D. 2002. Modifying gene expression programs by altering core promoter chromatin architecture. Cell 110:261–271.
- Lomvardas S, Thanos D. 2001. Nucleosome sliding via TBP DNA binding in vivo. Cell 106:685–696.
- Lorch Y, LaPointe JW, Kornberg RD. 1987. Nucleosomes inhibit the initiation of transcription but allow chain elongation with the displacement of histones. Cell 49:203–210.
- Lowary PT, Widom J. 1998. New DNA sequence rules for high affinity binding to histone octamer and sequence-directed nucleosome positioning. J. Mol. Biol. 276:19–42.
- Luger K, Mader AW, Richmond RK, Sargent DF, Richmond TJ. 1997. Crystal structure of the nucleosome core particle at 2.8 A resolution. Nature 389:251–260.
- Nady N, Min J, Kareta MS, Chedin F, Arrowsmith CH. 2008. A SPOT on the chromatin landscape? Histone peptide arrays as a tool for epigenetic research. Trends Biochem. Sci. 33:305–313.
- Orphanides G, Wu WH, Lane WS, Hampsey M, Reinberg D. 1999. The chromatin-specific transcription elongation factor FACT comprises human SPT16 and SSRP1 proteins. Nature 400:284–288.
- Pique-Regi R, et al. 2011. Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data. Genome Res. 21:447–455.
- Ramirez-Carrozzi VR, et al. 2009. A unifying model for the selective regulation of inducible transcription by CpG islands and nucleosome remodeling. Cell 138:114–128.
- Roh TY, Cuddapah S, Zhao K. 2005. Active chromatin domains are defined by acetylation islands revealed by genome-wide mapping. Genes Dev. 19:542–552.
- Sabo PJ, et al. 2004. Genome-wide identification of DNaseI hypersensitive sites using active chromatin sequence libraries. Proc. Natl. Acad. Sci. U. S. A. 101:4537–4542.
- Saunders A, et al. 2003. Tracking FACT and the RNA polymerase II elongation complex through chromatin in vivo. Science 301:1094–1096.
- Saxonov S, Berg P, Brutlag DL. 2006. A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters. Proc. Natl. Acad. Sci. U. S. A. 103:1412–1417.
- Shogren-Knaak M, et al. 2006. Histone H4–K16 acetylation controls chromatin structure and protein interactions. Science 311:844–847.
- Simon MD, et al. 2007. The site-specific installation of methyl-lysine analogs into recombinant histones. Cell 128:1003–1012.
- Smith E, Shilatifard A. 2010. The chromatin signaling pathway: diverse mechanisms of recruitment of histone-modifying enzymes and varied biological outcomes. Mol. Cell 40:689–701.
- Song J, Rechkoblit O, Bestor TH, Patel DJ. 2011. Structure of DNMT1-DNA complex reveals a role for autoinhibition in maintenance DNA methylation. Science 331:1036–1040.
- Strahl BD, et al. 2002. Set2 is a nucleosomal histone H3-selective methyltransferase that mediates transcriptional repression. Mol. Cell. Biol. 22:1298–1306.
- Taverna SD, Li H, Ruthenburg AJ, Allis CD, Patel DJ. 2007. How chromatin-binding modules interpret histone modifications: lessons from professional pocket pickers. Nat. Struct. Mol. Biol. 14:1025–1040.
- Tazi J, Bird A. 1990. Alternative chromatin structure at CpG islands. Cell 60:909–920.
- Thomson JP, et al. 2010. CpG islands influence chromatin structure via the CpG-binding protein Cfp1. Nature 464:1082–1086.
- Tillo D, Hughes TR. 2009. G+C content dominates intrinsic nucleosome occupancy. BMC Bioinformatics 10:442.
- Tillo D, et al. 2010. High nucleosome occupancy is encoded at human regulatory sequences. PLoS One 5:e9129.
- Tsumura A, et al. 2006. Maintenance of self-renewal ability of mouse embryonic stem cells in the absence of DNA methyltransferases Dnmt1, Dnmt3a and Dnmt3b. Genes Cells 11:805–814.
- Vermeulen M, et al. 2010. Quantitative interaction proteomics and genome-wide profiling of epigenetic histone marks and their readers. Cell 142:967–980.
- Wysocka J, et al. 2006. A PHD finger of NURF couples histone H3 lysine 4 trimethylation with chromatin remodelling. Nature 442:86–90.
- Xi H, et al. 2007. Identification and characterization of cell type-specific and ubiquitous chromatin regulatory structures in the human genome. PLoS Genet. 3:e136.