CpG island chromatin

References

• Lister R, Pelizzola M, Dowen RH, Hawkins RD, Hon G, Tonti-Filippini J, et al. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 2009; 462:315 - 322
   PubMed Web of Science ®Google Scholar
• Klose RJ, Bird AP. Genomic DNA methylation: the mark and its mediators. Trends Biochem Sci 2006; 31:89 - 97
   PubMed Web of Science ®Google Scholar
• Bird A, Taggart M, Frommer M, Miller OJ, Macleod D. A fraction of the mouse genome that is derived from islands of nonmethylated, CpG-rich DNA. Cell 1985; 40:91 - 99
   PubMed Web of Science ®Google Scholar
• Cooper DN, Taggart MH, Bird AP. Unmethylated domains in vertebrate DNA. Nucleic Acids Res 1983; 11:647 - 658
   PubMed Web of Science ®Google Scholar
• Illingworth RS, Bird AP. CpG islands—‘a rough guide’. FEBS Lett 2009; 583:1713 - 1720
   PubMed Web of Science ®Google Scholar
• Sandelin A, Carninci P, Lenhard B, Ponjavic J, Hayashizaki Y, Hume DA. Mammalian RNA polymerase II core promoters: insights from genome-wide studies. Nat Rev Genet 2007; 8:424 - 436
   PubMed Web of Science ®Google Scholar
• Larsen F, Gundersen G, Lopez R, Prydz H. CpG islands as gene markers in the human genome. Genomics 1992; 13:1095 - 1107
   PubMed Web of Science ®Google Scholar
• Zhu J, He F, Hu S, Yu J. On the nature of human housekeeping genes. Trends Genet 2008; 24:481 - 484
   PubMed Web of Science ®Google Scholar
• Bell AC, Felsenfeld G. Methylation of a CTCF-dependent boundary controls imprinted expression of the Igf2 gene. Nature 2000; 405:482 - 485
   PubMed Web of Science ®Google Scholar
• Mancini DN, Singh SM, Archer TK, Rodenhiser DI. Site-specific DNA methylation in the neurofibromatosis (NF1) promoter interferes with binding of CREB and SP1 transcription factors. Oncogene 1999; 18:4108 - 4119
   PubMed Web of Science ®Google Scholar
• Renda M, Baglivo I, Burgess-Beusse B, Esposito S, Fattorusso R, Felsenfeld G, et al. Critical DNA binding interactions of the insulator protein CTCF: a small number of zinc fingers mediate strong binding and a single finger-DNA interaction controls binding at imprinted loci. J Biol Chem 2007; 282:33336 - 33345
   PubMed Web of Science ®Google Scholar
• Zhu WG, Srinivasan K, Dai Z, Duan W, Druhan LJ, Ding H, et al. Methylation of adjacent CpG sites affects Sp1/Sp3 binding and activity in the p21(Cip1) promoter. Mol Cell Biol 2003; 23:4056 - 4065
   PubMed Web of Science ®Google Scholar
• Iguchi-Ariga SM, Schaffner W. CpG methylation of the cAMP-responsive enhancer/promoter sequence TGA CGT CA abolishes specific factor binding as well as transcriptional activation. Genes Dev 1989; 3:612 - 619
   PubMed Web of Science ®Google Scholar
• Impey S, McCorkle SR, Cha-Molstad H, Dwyer JM, Yochum GS, Boss JM, et al. Defining the CREB regulon: a genome-wide analysis of transcription factor regulatory regions. Cell 2004; 119:1041 - 1054
   PubMed Web of Science ®Google Scholar
• Kim TH, Abdullaev ZK, Smith AD, Ching KA, Loukinov DI, Green RD, et al. Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome. Cell 2007; 128:1231 - 1245
   PubMed Web of Science ®Google Scholar
• Reed BD, Charos AE, Szekely AM, Weissman SM, Snyder M. Genome-wide occupancy of SREBP1 and its partners NFY and SP1 reveals novel functional roles and combinatorial regulation of distinct classes of genes. PLoS Genet 2008; 4:e1000133
   PubMed Web of Science ®Google Scholar
• Voo KS, Carlone DL, Jacobsen BM, Flodin A, Skalnik DG. Cloning of a mammalian transcriptional activator that binds unmethylated CpG motifs and shares a CXXC domain with DNA methyltransferase, human trithorax and methyl-CpG binding domain protein 1. Mol Cell Biol 2000; 20:2108 - 2121
   PubMed Web of Science ®Google Scholar
• Lee JH, Skalnik DG. CpG-binding protein (CXXC finger protein 1) is a component of the mammalian Set1 histone H3-Lys4 methyltransferase complex, the analogue of the yeast Set1/COMPASS complex. J Biol Chem 2005; 280:41725 - 41731
   PubMed Web of Science ®Google Scholar
• Glaser S, Lubitz S, Loveland KL, Ohbo K, Robb L, Schwenk F. The histone 3 lysine 4 methyltransferase, Mll2, is only required briefly in development and spermatogenesis. Epigenetics Chromatin 2009; 2:5
   PubMed Web of Science ®Google Scholar
• Blackledge NP, Zhou JC, Tolstorukov MY, Farcas AM, Park PJ, Klose RJ. CpG islands recruit a histone H3 lysine 36 demethylase. Mol Cell 2010; 38:179 - 190
   PubMed Web of Science ®Google Scholar
• Thomson JP, Skene PJ, Selfridge J, Clouaire T, Guy J, Webb S, et al. CpG islands influence chromatin structure via the CpG-binding protein Cfp1. Nature 2010; 464:1082 - 1086
   PubMed Web of Science ®Google Scholar
• Tsukada Y, Fang J, Erdjument-Bromage H, Warren ME, Borchers CH, Tempst P, et al. Histone demethylation by a family of JmjC domain-containing proteins. Nature 2006; 439:811 - 816
   PubMed Web of Science ®Google Scholar
• Garcia BA, Thomas CE, Kelleher NL, Mizzen CA. Tissue-specific expression and post-translational modification of histone H3 variants. J Proteome Res 2008; 7:4225 - 4236
   PubMed Web of Science ®Google Scholar
• Peters AH, Kubicek S, Mechtler K, O'Sullivan RJ, Derijck AA, Perez-Burgos L, et al. Partitioning and plasticity of repressive histone methylation states in mammalian chromatin. Mol Cell 2003; 12:1577 - 1589
   PubMed Web of Science ®Google Scholar
• Robin P, Fritsch L, Philipot O, Svinarchuk F, Ait-Si-Ali S. Post-translational modifications of histones H3 and H4 associated with the histone methyltransferases Suv391h and G9a. Genome Biol 2007; 8:270
   Web of Science ®Google Scholar
• Mikkelsen TS, Ku M, Jaffe DB, Issac B, Lieberman E, Giannoukos G, et al. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 2007; 448:553 - 560
   PubMed Web of Science ®Google Scholar
• Guenther MG, Levine SS, Boyer LA, Jaenisch R, Young RA. A chromatin landmark and transcription initiation at most promoters in human cells. Cell 2007; 130:77 - 88
   PubMed Web of Science ®Google Scholar
• Cuadrado M, Sacristan M, Antequera F. Species-specific organization of CpG island promoters at mammalian homologous genes. EMBO Rep 2001; 2:586 - 592
   PubMed Web of Science ®Google Scholar
• Vermeulen M, Mulder KW, Denissov S, Pijnappel WW, van Schaik FM, Varier RA, et al. Selective anchoring of TFIID to nucleosomes by trimethylation of histone H3 lysine 4. Cell 2007; 131:58 - 69
   PubMed Web of Science ®Google Scholar
• Wysocka J, Swigut T, Xiao H, Milne TA, Kwon SY, Landry J, et al. A PHD finger of NURF couples histone H3 lysine 4 trimethylation with chromatin remodelling. Nature 2006; 442:86 - 90
   PubMed Web of Science ®Google Scholar
• Saksouk N, Avvakumov N, Champagne KS, Hung T, Doyon Y, Cayrou C, et al. HBO1 HAT complexes target chromatin throughout gene coding regions via multiple PHD finger interactions with histone H3 tail. Mol Cell 2009; 33:257 - 265
   PubMed Web of Science ®Google Scholar
• Carrozza MJ, Li B, Florens L, Suganuma T, Swanson SK, Lee KK, et al. Histone H3 methylation by Set2 directs deacetylation of coding regions by Rpd3S to suppress spurious intragenic transcription. Cell 2005; 123:581 - 592
   PubMed Web of Science ®Google Scholar
• Li B, Jackson J, Simon MD, Fleharty B, Gogol M, Seidel C, et al. Histone H3 lysine 36 dimethylation (H3K36me2) is sufficient to recruit the Rpd3s histone deacetylase complex and to repress spurious transcription. J Biol Chem 2009; 284:7970 - 7976
   PubMed Web of Science ®Google Scholar
• Strahl BD, Grant PA, Briggs SD, Sun ZW, Bone JR, Caldwell JA, et al. Set2 is a nucleosomal histone H3-selective methyltransferase that mediates transcriptional repression. Mol Cell Biol 2002; 22:1298 - 1306
   PubMed Web of Science ®Google Scholar
• Youdell ML, Kizer KO, Kisseleva-Romanova E, Fuchs SM, Duro E, Strahl BD, et al. Roles for Ctk1 and Spt6 in regulating the different methylation states of histone H3 lysine 36. Mol Cell Biol 2008; 28:4915 - 4926
   PubMedGoogle Scholar
• Tazi J, Bird A. Alternative chromatin structure at CpG islands. Cell 1990; 60:909 - 920
   PubMed Web of Science ®Google Scholar
• Croston GE, Kerrigan LA, Lira LM, Marshak DR, Kadonaga JT. Sequence-specific antirepression of histone H1-mediated inhibition of basal RNA polymerase II transcription. Science 1991; 251:643 - 649
   PubMed Web of Science ®Google Scholar
• Levine A, Yeivin A, Ben-Asher E, Aloni Y, Razin A. Histone H1-mediated inhibition of transcription initiation of methylated templates in vitro. J Biol Chem 1993; 268:21754 - 21759
   PubMed Web of Science ®Google Scholar
• Shimamura A, Sapp M, Rodriguez-Campos A, Worcel A. Histone H1 represses transcription from minichromosomes assembled in vitro. Mol Cell Biol 1989; 9:5573 - 5584
   PubMedGoogle Scholar
• Wolffe AP. Dominant and specific repression of Xenopus oocyte 5S RNA genes and satellite I DNA by histone H1. EMBO J 1989; 8:527 - 537
   PubMed Web of Science ®Google Scholar
• Thoma F, Koller T, Klug A. Involvement of histone H1 in the organization of the nucleosome and of the salt-dependent superstructures of chromatin. J Cell Biol 1979; 83:403 - 427
   PubMed Web of Science ®Google Scholar
• Core LJ, Waterfall JJ, Lis JT. Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science 2008; 322:1845 - 1848
   PubMed Web of Science ®Google Scholar
• Seila AC, Calabrese JM, Levine SS, Yeo GW, Rahl PB, Flynn RA, et al. Divergent transcription from active promoters. Science 2008; 322:1849 - 1851
   PubMed Web of Science ®Google Scholar
• Kanhere A, Viiri K, Araujo CC, Rasaiyaah J, Bouwman RD, Whyte WA, et al. Short RNAs are transcribed from repressed polycomb target genes and interact with polycomb repressive complex-2. Mol Cell 2010; 38:675 - 688
   PubMed Web of Science ®Google Scholar
• He Y, Vogelstein B, Velculescu VE, Papadopoulos N, Kinzler KW. The antisense transcriptomes of human cells. Science 2008; 322:1855 - 1857
   PubMed Web of Science ®Google Scholar
• Preker P, Nielsen J, Kammler S, Lykke-Andersen S, Christensen MS, Mapendano CK, et al. RNA exosome depletion reveals transcription upstream of active human promoters. Science 2008; 322:1851 - 1854
   PubMed Web of Science ®Google Scholar
• Ramirez-Carrozzi VR, Braas D, Bhatt DM, Cheng CS, Hong C, Doty KR, et al. A unifying model for the selective regulation of inducible transcription by CpG islands and nucleosome remodeling. Cell 2009; 138:114 - 128
   PubMed Web of Science ®Google Scholar
• Angel P, Hattori K, Smeal T, Karin M. The jun proto-oncogene is positively autoregulated by its product, Jun/AP-1. Cell 1988; 55:875 - 885
   PubMed Web of Science ®Google Scholar
• Yao J, Mackman N, Edgington TS, Fan ST. Lipopolysaccharide induction of the tumor necrosis factor-alpha promoter in human monocytic cells. Regulation by Egr-1, c-Jun and NFkappaB transcription factors. J Biol Chem 1997; 272:17795 - 17801
   PubMed Web of Science ®Google Scholar
• Bernstein BE, Mikkelsen TS, Xie X, Kamal M, Huebert DJ, Cuff J, et al. A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell 2006; 125:315 - 326
   PubMed Web of Science ®Google Scholar
• Tanay A, O'Donnell AH, Damelin M, Bestor TH. Hyperconserved CpG domains underlie Polycomb-binding sites. Proc Natl Acad Sci USA 2007; 104:5521 - 5526
   PubMed Web of Science ®Google Scholar
• Stock JK, Giadrossi S, Casanova M, Brookes E, Vidal M, Koseki H, et al. Ring1-mediated ubiquitination of H2A restrains poised RNA polymerase II at bivalent genes in mouse ES cells. Nat Cell Biol 2007; 9:1428 - 1435
   PubMed Web of Science ®Google Scholar
• Meehan RR, Lewis JD, McKay S, Kleiner EL, Bird AP. Identification of a mammalian protein that binds specifically to DNA containing methylated CpGs. Cell 1989; 58:499 - 507
   PubMed Web of Science ®Google Scholar
• Nan X, Ng HH, Johnson CA, Laherty CD, Turner BM, Eisenman RN, et al. Transcriptional repression by the methyl-CpG-binding protein MeCP2 involves a histone deacetylase complex. Nature 1998; 393:386 - 389
   PubMed Web of Science ®Google Scholar
• Schlesinger Y, Straussman R, Keshet I, Farkash S, Hecht M, Zimmerman J, et al. Polycomb-mediated methylation on Lys27 of histone H3 pre-marks genes for de novo methylation in cancer. Nat Genet 2007; 39:232 - 236
   PubMed Web of Science ®Google Scholar
• Vire E, Brenner C, Deplus R, Blanchon L, Fraga M, Didelot C, et al. The Polycomb group protein EZH2 directly controls DNA methylation. Nature 2006; 439:871 - 874
   PubMed Web of Science ®Google Scholar
• Delgado S, Gomez M, Bird A, Antequera F. Initiation of DNA replication at CpG islands in mammalian chromosomes. EMBO J 1998; 17:2426 - 2435
   PubMed Web of Science ®Google Scholar
• Sequeira-Mendes J, Diaz-Uriarte R, Apedaile A, Huntley D, Brockdorff N, Gomez M. Transcription initiation activity sets replication origin efficiency in mammalian cells. PLoS Genet 2009; 5:e1000446
   PubMed Web of Science ®Google Scholar
• Gomez M, Antequera F. Overreplication of short DNA regions during S phase in human cells. Genes Dev 2008; 22:375 - 385
   PubMed Web of Science ®Google Scholar
• Kriaucionis S, Heintz N. The nuclear DNA base 5-hydroxymethylcytosine is present in Purkinje neurons and the brain. Science 2009; 324:929 - 930
   PubMed Web of Science ®Google Scholar
• Tahiliani M, Koh KP, Shen Y, Pastor WA, Bandukwala H, Brudno Y, et al. Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science 2009; 324:930 - 935
   PubMed Web of Science ®Google Scholar
• Ito S, D'Alessio AC, Taranova OV, Hong K, Sowers LC, Zhang Y. Role of Tet proteins in 5 mC to 5 hmC conversion, ES-cell self-renewal and inner cell mass specification. Nature 2010; 466:1129 - 1133
   PubMed Web of Science ®Google Scholar