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The Role of DNA Methylation and Histone Modifications in Transcriptional Regulation in Humans

  • Jaime L. Miller
  • Patrick A. GrantEmail author
Chapter
Part of the Subcellular Biochemistry book series (SCBI, volume 61)

Abstract

Although the field of genetics has grown by leaps and bounds within the last decade due to the completion and availability of the human genome sequence, transcriptional regulation still cannot be explained solely by an individual’s DNA sequence. Complex coordination and communication between a plethora of well-conserved chromatin modifying factors are essential for all organisms. Regulation of gene expression depends on histone post translational modifications (HPTMs), DNA methylation, histone variants, remodeling enzymes, and effector proteins that influence the structure and function of chromatin, which affects a broad spectrum of cellular processes such as DNA repair, DNA replication, growth, and proliferation. If mutated or deleted, many of these factors can result in human disease at the level of transcriptional regulation. The common goal of recent studies is to understand disease states at the stage of altered gene expression. Utilizing information gained from new high-throughput techniques and analyses will aid biomedical research in the development of treatments that work at one of the most basic levels of gene expression, chromatin. This chapter will discuss the effects of and mechanism by which histone modifications and DNA methylation affect transcriptional regulation.

Keywords

Histone Modification H3K79 Methylation Imprint Control Region Epigenetic Landscape Repressive Mark 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

References

  1. Agger K, Cloos PA, Christensen J, Pasini D, Rose S, Rappsilber J et al (2007) UTX and JMJD3 are histone H3K27 demethylases involved in HOX gene regulation and development. Nature 449(7163):731–734PubMedGoogle Scholar
  2. Allis CD, Bowen JK, Abraham GN, Glover CV, Gorovsky MA (1980) Proteolytic processing of histone H3 in chromatin: a physiologically regulated event in tetrahymena micronuclei. Cell 20(1):55–64PubMedGoogle Scholar
  3. Antequera F, Bird A (1993) Number of CpG islands and genes in human and mouse. Proc Natl Acad Sci USA 90(24):11995–11999PubMedGoogle Scholar
  4. Baker SP, Phillips J, Anderson S, Qiu Q, Shabanowitz J, Smith MM et al (2010) Histone H3 thr 45 phosphorylation is a replication-associated post-translational modification in S. cerevisiae. Nat Cell Biol 12(3):294–298PubMedGoogle Scholar
  5. Bannister AJ, Kouzarides T (2011) Regulation of chromatin by histone modifications. Cell Res 21(3):381–395PubMedGoogle Scholar
  6. Bannister AJ, Schneider R, Kouzarides T (2002) Histone methylation: dynamic or static? Cell 109(7):801–806PubMedGoogle Scholar
  7. Bardwell VJ, Treisman R (1994) The POZ domain: a conserved protein-protein interaction motif. Genes Dev 8(14):1664–1677PubMedGoogle Scholar
  8. Barski A, Cuddapah S, Cui K, Roh TY, Schones DE, Wang Z et al (2007) High-resolution profiling of histone methylations in the human genome. Cell 129(4):823–837PubMedGoogle Scholar
  9. Bell AC, Felsenfeld G (2000) Methylation of a CTCF-dependent boundary controls imprinted expression of the Igf2 gene. Nature 405(6785):482–485PubMedGoogle Scholar
  10. Bernstein BE, Mikkelsen TS, Xie X, Kamal M, Huebert DJ, Cuff J et al (2006) A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell 125(2):315–326PubMedGoogle Scholar
  11. Bestor T, Laudano A, Mattaliano R, Ingram V (1988) Cloning and sequencing of a cDNA encoding DNA methyltransferase of mouse cells. The carboxyl-terminal domain of the mammalian enzymes is related to bacterial restriction methyltransferases. J Mol Biol 203(4):971–983PubMedGoogle Scholar
  12. Bird A (2002) DNA methylation patterns and epigenetic memory. Genes Dev 16(1):6–21PubMedGoogle Scholar
  13. Bird AP, Wolffe AP (1999) Methylation-induced repression–belts, braces, and chromatin. Cell 99(5):451–454PubMedGoogle Scholar
  14. Black JC, Whetstine JR (2011) Chromatin landscape: methylation beyond transcription. Epigenetics Off J DNA Methylation Soc 6(1):9–15Google Scholar
  15. Bostick M, Kim JK, Esteve PO, Clark A, Pradhan S, Jacobsen SE (2007) UHRF1 plays a role in maintaining DNA methylation in mammalian cells. Science (New York, NY) 317(5845):1760–1764Google Scholar
  16. Brenner C, Deplus R, Didelot C, Loriot A, Vire E, De Smet C et al (2005) Myc represses transcription through recruitment of DNA methyltransferase corepressor. EMBO J 24(2):336–346PubMedGoogle Scholar
  17. Brown CE, Howe L, Sousa K, Alley SC, Carrozza MJ, Tan S et al (2001) Recruitment of HAT complexes by direct activator interactions with the ATM-related Tra1 subunit. Science (New York, NY) 292(5525):2333–2337Google Scholar
  18. Brownell JE, Zhou J, Ranalli T, Kobayashi R, Edmondson DG, Roth SY et al (1996) Tetrahymena histone acetyltransferase A: a homolog to yeast Gcn5p linking histone acetylation to gene activation. Cell 84(6):843–851PubMedGoogle Scholar
  19. Campion J, Milagro FI, Martinez JA (2009) Individuality and epigenetics in obesity. Obes Rev Off J Int Assoc Study Obes 10(4):383–392Google Scholar
  20. Carrozza MJ, Li B, Florens L, Suganuma T, Swanson SK, Lee KK et al (2005) Histone H3 methylation by Set2 directs deacetylation of coding regions by Rpd3S to suppress spurious intragenic transcription. Cell 123(4):581–592PubMedGoogle Scholar
  21. Champagne KS, Kutateladze TG (2009) Structural insight into histone recognition by the ING PHD fingers. Curr Drug Targets 10(5):432–441PubMedGoogle Scholar
  22. Chen C, Nott TJ, Jin J, Pawson T (2011) Deciphering arginine methylation: tudor tells the tale. Nat Rev Mol Cell Biol 12(10):629–642PubMedGoogle Scholar
  23. Clark SJ, Harrison J, Frommer M (1995) CpNpG methylation in mammalian cells. Nat Genet 10(1):20–27PubMedGoogle Scholar
  24. Cloos PA, Christensen J, Agger K, Maiolica A, Rappsilber J, Antal T et al (2006) The putative oncogene GASC1 demethylates tri- and dimethylated lysine 9 on histone H3. Nature 442(7100):307–311PubMedGoogle Scholar
  25. Cui K, Zang C, Roh TY, Schones DE, Childs RW, Peng W et al (2009) Chromatin signatures in multipotent human hematopoietic stem cells indicate the fate of bivalent genes during differentiation. Cell Stem Cell 4(1):80–93PubMedGoogle Scholar
  26. Cuthbert GL, Daujat S, Snowden AW, Erdjument-Bromage H, Hagiwara T, Yamada M et al (2004) Histone deimination antagonizes arginine methylation. Cell 118(5):545–553PubMedGoogle Scholar
  27. Delaval K, Wagschal A, Feil R (2006) Epigenetic deregulation of imprinting in congenital diseases of aberrant growth. BioEssays News Rev Mol Cell Dev Biol 28(5):453–459Google Scholar
  28. Di Croce L, Raker VA, Corsaro M, Fazi F, Fanelli M, Faretta M et al (2002) Methyltransferase recruitment and DNA hypermethylation of target promoters by an oncogenic transcription factor. Science (New York, NY) 295(5557):1079–1082Google Scholar
  29. Doi A, Park IH, Wen B, Murakami P, Aryee MJ, Irizarry R et al (2009) Differential methylation of tissue- and cancer-specific CpG island shores distinguishes human induced pluripotent stem cells, embryonic stem cells and fibroblasts. Nat Genet 41(12):1350–1353PubMedGoogle Scholar
  30. Duncan EM, Muratore-Schroeder TL, Cook RG, Garcia BA, Shabanowitz J, Hunt DF et al (2008) Cathepsin L proteolytically processes histone H3 during mouse embryonic stem cell differentiation. Cell 135(2):284–294PubMedGoogle Scholar
  31. Ehrlich M, Gama-Sosa MA, Huang LH, Midgett RM, Kuo KC, McCune RA et al (1982) Amount and distribution of 5-methylcytosine in human DNA from different types of tissues of cells. Nucleic Acids Res 10(8):2709–2721PubMedGoogle Scholar
  32. Ernst J, Kellis M (2010) Discovery and characterization of chromatin states for systematic annotation of the human genome. Nat Biotechnol 28(8):817–825PubMedGoogle Scholar
  33. Esteller M (2007) Cancer epigenomics: DNA methylomes and histone-modification maps. Nat Rev Genet 8(4):286–298PubMedGoogle Scholar
  34. Feng Q, Wang H, Ng HH, Erdjument-Bromage H, Tempst P, Struhl K et al (2002) Methylation of H3-lysine 79 is mediated by a new family of HMTases without a SET domain. Curr Biol (CB) 12(12):1052–1058Google Scholar
  35. Ficz G, Branco MR, Seisenberger S, Santos F, Krueger F, Hore TA et al (2011) Dynamic regulation of 5-hydroxymethylcytosine in mouse ES cells and during differentiation. Nature 473(7347):398–402PubMedGoogle Scholar
  36. Fischle W, Tseng BS, Dormann HL, Ueberheide BM, Garcia BA, Shabanowitz J et al (2005) Regulation of HP1-chromatin binding by histone H3 methylation and phosphorylation. Nature 438(7071):1116–1122PubMedGoogle Scholar
  37. Fodor BD, Kubicek S, Yonezawa M, O’Sullivan RJ, Sengupta R, Perez-Burgos L et al (2006) Jmjd2b antagonizes H3K9 trimethylation at pericentric heterochromatin in mammalian cells. Genes Dev 20(12):1557–1562PubMedGoogle Scholar
  38. Fraga MF, Ballestar E, Paz MF, Ropero S, Setien F, Ballestar ML et al (2005) Epigenetic differences arise during the lifetime of monozygotic twins. Proc Natl Acad Sci USA 102(30):10604–10609PubMedGoogle Scholar
  39. Garcia-Bassets I, Kwon YS, Telese F, Prefontaine GG, Hutt KR, Cheng CS et al (2007) Histone methylation-dependent mechanisms impose ligand dependency for gene activation by nuclear receptors. Cell 128(3):505–518PubMedGoogle Scholar
  40. Glozak MA, Sengupta N, Zhang X, Seto E (2005) Acetylation and deacetylation of non-histone proteins. Gene 363:15–23PubMedGoogle Scholar
  41. Govind CK, Qiu H, Ginsburg DS, Ruan C, Hofmeyer K, Hu C et al (2010) Phosphorylated Pol II CTD recruits multiple HDACs, including Rpd3C(S), for methylation-dependent deacetylation of ORF nucleosomes. Mol Cell 39(2):234–246PubMedGoogle Scholar
  42. Grant PA, Duggan L, Cote J, Roberts SM, Brownell JE, Candau R et al (1997) Yeast Gcn5 functions in two multisubunit complexes to acetylate nucleosomal histones: characterization of an ada complex and the SAGA (Spt/Ada) complex. Genes Dev 11(13):1640–1650PubMedGoogle Scholar
  43. Grant PA, Schieltz D, Pray-Grant MG, Steger DJ, Reese JC, Yates JR 3rd et al (1998) A subset of TAF(II)s are integral components of the SAGA complex required for nucleosome acetylation and transcriptional stimulation. Cell 94(1):45–53PubMedGoogle Scholar
  44. Greeson NT, Sengupta R, Arida AR, Jenuwein T, Sanders SL (2008) Di-methyl H4 lysine 20 targets the checkpoint protein Crb2 to sites of DNA damage. J Biol Chem 283(48):33168–33174PubMedGoogle Scholar
  45. Guelen L, Pagie L, Brasset E, Meuleman W, Faza MB, Talhout W et al (2008) Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions. Nature 453(7197):948–951PubMedGoogle Scholar
  46. Hampsey M, Reinberg D (2003) Tails of intrigue: phosphorylation of RNA polymerase II mediates histone methylation. Cell 113(4):429–432PubMedGoogle Scholar
  47. Hark AT, Schoenherr CJ, Katz DJ, Ingram RS, Levorse JM, Tilghman SM (2000) CTCF mediates methylation-sensitive enhancer-blocking activity at the H19/Igf2 locus. Nature 405(6785):486–489PubMedGoogle Scholar
  48. Hassan AH, Prochasson P, Neely KE, Galasinski SC, Chandy M, Carrozza MJ et al (2002) Function and selectivity of bromodomains in anchoring chromatin-modifying complexes to promoter nucleosomes. Cell 111(3):369–379PubMedGoogle Scholar
  49. Hatada I, Fukasawa M, Kimura M, Morita S, Yamada K, Yoshikawa T et al (2006) Genome-wide profiling of promoter methylation in human. Oncogene 25(21):3059–3064PubMedGoogle Scholar
  50. Hebbes TR, Thorne AW, Crane-Robinson C (1988) A direct link between core histone acetylation and transcriptionally active chromatin. EMBO J 7(5):1395–1402PubMedGoogle Scholar
  51. Heintzman ND, Stuart RK, Hon G, Fu Y, Ching CW, Hawkins RD et al (2007) Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat Genet 39(3):311–318Google Scholar
  52. Heitz E (1929) Heterochromatin, chromocentren, chromomenen. Berichte der Deutschen Botanischen Gesellschaft 47:274–284Google Scholar
  53. Hendrich B, Tweedie S (2003) The methyl-CpG binding domain and the evolving role of DNA methylation in animals. Trends Genet (TIG) 19(5):269–277Google Scholar
  54. Hendrich B, Hardeland U, Ng HH, Jiricny J, Bird A (1999) The thymine glycosylase MBD4 can bind to the product of deamination at methylated CpG sites. Nature 401(6750):301–304PubMedGoogle Scholar
  55. Hervouet E, Vallette FM, Cartron PF (2009) Dnmt3/transcription factor interactions as crucial players in targeted DNA methylation. Epigenet Off J DNA Methyl Soc 4(7):487–499PubMedGoogle Scholar
  56. Huyen Y, Zgheib O, Ditullio RA Jr, Gorgoulis VG, Zacharatos P, Petty TJ et al (2004) Methylated lysine 79 of histone H3 targets 53BP1 to DNA double-strand breaks. Nature 432(7015):406–411PubMedGoogle Scholar
  57. Iioka H, Doerner SK, Tamai K (2009) Kaiso is a bimodal modulator for Wnt/beta-catenin signaling. FEBS Lett 583(4):627–632PubMedGoogle Scholar
  58. Illingworth R, Kerr A, Desousa D, Jorgensen H, Ellis P, Stalker J et al (2008) A novel CpG island set identifies tissue-specific methylation at developmental gene loci. PLoS Biol 6(1):e22PubMedGoogle Scholar
  59. Iqbal K, Jin SG, Pfeifer GP, Szabo PE (2011) Reprogramming of the paternal genome upon fertilization involves genome-wide oxidation of 5-methylcytosine. Proc Natl Acad Sci USA 108(9):3642–3647PubMedGoogle Scholar
  60. Issa JP (2000) CpG-island methylation in aging and cancer. Curr Top Microbiol Immunol 249:101–118PubMedGoogle Scholar
  61. Issaeva I, Zonis Y, Rozovskaia T, Orlovsky K, Croce CM, Nakamura T et al (2007) Knockdown of ALR (MLL2) reveals ALR target genes and leads to alterations in cell adhesion and growth. Mol Cell Biol 27(5):1889–1903PubMedGoogle Scholar
  62. Ito S, D’Alessio AC, Taranova OV, Hong K, Sowers LC, Zhang Y (2010) Role of tet proteins in 5mC to 5hmC conversion, ES-cell self-renewal and inner cell mass specification. Nature 466(7310):1129–1133PubMedGoogle Scholar
  63. Iwase S, Lan F, Bayliss P, de la Torre-Ubieta L, Huarte M, Qi HH et al (2007) The X-linked mental retardation gene SMCX/JARID1C defines a family of histone H3 lysine 4 demethylases. Cell 128(6):1077–1088PubMedGoogle Scholar
  64. Jacobson RH, Ladurner AG, King DS, Tjian R (2000) Structure and function of a human TAFII250 double bromodomain module. Science (New York, NY) 288(5470):1422–1425Google Scholar
  65. Javierre BM, Fernandez AF, Richter J, Al-Shahrour F, Martin-Subero JI, Rodriguez-Ubreva J et al (2010) Changes in the pattern of DNA methylation associate with twin discordance in systemic lupus erythematosus. Genome Res 20(2):170–179PubMedGoogle Scholar
  66. Jenuwein T (2001) Re-SET-ting heterochromatin by histone methyltransferases. Trends Cell Biol 11(6):266–273PubMedGoogle Scholar
  67. Jenuwein T, Allis CD (2001) Translating the histone code. Science (New York, NY) 293(5532):1074–1080Google Scholar
  68. Jones PA, Wolkowicz MJ, Rideout WM 3rd, Gonzales FA, Marziasz CM, Coetzee GA et al (1990) De novo methylation of the MyoD1 CpG island during the establishment of immortal cell lines. Proc Natl Acad Sci USA 87(16):6117–6121PubMedGoogle Scholar
  69. Jorgensen HF, Ben-Porath I, Bird AP (2004) Mbd1 is recruited to both methylated and nonmethylated CpGs via distinct DNA binding domains. Mol Cell Biol 24(8):3387–3395PubMedGoogle Scholar
  70. Joshi AA, Struhl K (2005) Eaf3 chromodomain interaction with methylated H3-K36 links histone deacetylation to Pol II elongation. Mol Cell 20(6):971–978PubMedGoogle Scholar
  71. Josse J, Kaiser AD, Kornberg A (1961) Enzymatic synthesis of deoxyribonucleic acid. VIII. Frequencies of nearest neighbor base sequences in deoxyribonucleic acid. J Biol Chem 236:864–875PubMedGoogle Scholar
  72. Kacem S, Feil R (2009) Chromatin mechanisms in genomic imprinting. Mamm Genome Off J Int Mamm Genome Soc 20(9–10):544–556Google Scholar
  73. Kanduri C, Pant V, Loukinov D, Pugacheva E, Qi CF, Wolffe A et al (2000) Functional association of CTCF with the insulator upstream of the H19 gene is parent of origin-specific and methylation-sensitive. Curr Biol (CB) 10(14):853–856Google Scholar
  74. Karlic R, Chung HR, Lasserre J, Vlahovicek K, Vingron M (2010) Histone modification levels are predictive for gene expression. Proc Natl Acad Sci USA 107(7):2926–2931PubMedGoogle Scholar
  75. Kaufman PD, Rando OJ (2010) Chromatin as a potential carrier of heritable information. Curr Opin Cell Biol 22(3):284–290PubMedGoogle Scholar
  76. Keogh MC, Podolny V, Buratowski S (2003) Bur1 kinase is required for efficient transcription elongation by RNA polymerase II. Mol Cell Biol 23(19):7005–7018PubMedGoogle Scholar
  77. Keogh MC, Kurdistani SK, Morris SA, Ahn SH, Podolny V, Collins SR et al (2005) Cotranscriptional set2 methylation of histone H3 lysine 36 recruits a repressive Rpd3 complex. Cell 123(4):593–605PubMedGoogle Scholar
  78. Kim H, Kang K, Kim J (2009a) AEBP2 as a potential targeting protein for polycomb repression complex PRC2. Nucleic Acids Res 37(9):2940–2950PubMedGoogle Scholar
  79. Kim J, Guermah M, McGinty RK, Lee JS, Tang Z, Milne TA et al (2009b) RAD6-mediated transcription-coupled H2B ubiquitylation directly stimulates H3K4 methylation in human cells. Cell 137(3):459–471PubMedGoogle Scholar
  80. Klose RJ, Bird AP (2006) Genomic DNA methylation: the mark and its mediators. Trends Biochem Sci 31(2):89–97PubMedGoogle Scholar
  81. Klose RJ, Yamane K, Bae Y, Zhang D, Erdjument-Bromage H, Tempst P et al (2006) The transcriptional repressor JHDM3A demethylates trimethyl histone H3 lysine 9 and lysine 36. Nature 442(7100):312–316PubMedGoogle Scholar
  82. Klose RJ, Yan Q, Tothova Z, Yamane K, Erdjument-Bromage H, Tempst P et al (2007) The retinoblastoma binding protein RBP2 is an H3K4 demethylase. Cell 128(5):889–900PubMedGoogle Scholar
  83. Koh KP, Yabuuchi A, Rao S, Huang Y, Cunniff K, Nardone J et al (2011) Tet1 and Tet2 regulate 5-hydroxymethylcytosine production and cell lineage specification in mouse embryonic stem cells. Cell Stem Cell 8(2):200–213PubMedGoogle Scholar
  84. Kolasinska-Zwierz P, Down T, Latorre I, Liu T, Liu XS, Ahringer J (2009) Differential chromatin marking of introns and expressed exons by H3K36me3. Nat Genet 41(3):376–381PubMedGoogle Scholar
  85. Kouzarides T (2007) Chromatin modifications and their function. Cell 128(4):693–705PubMedGoogle Scholar
  86. Kouzarides T, Berger S (2007) Chromatin modifications and their mechanisms of action. In: Allis CD, Jenuwein T, Reinberg D (eds) Epigenetics. Cold Spring Harbor Laboratory Press, Plainview, pp 191–206Google Scholar
  87. Kriaucionis S, Heintz N (2009) The nuclear DNA base 5-hydroxymethylcytosine is present in Purkinje neurons and the brain. Science (New York, NY) 324(5929):929–930Google Scholar
  88. Krogan NJ, Kim M, Tong A, Golshani A, Cagney G, Canadien V et al (2003) Methylation of histone H3 by Set2 in Saccharomyces cerevisiae is linked to transcriptional elongation by RNA polymerase II. Mol Cell Biol 23(12):4207–4218PubMedGoogle Scholar
  89. Lange M, Kaynak B, Forster UB, Tonjes M, Fischer JJ, Grimm C et al (2008) Regulation of muscle development by DPF3, a novel histone acetylation and methylation reader of the BAF chromatin remodeling complex. Genes Dev 22(17):2370–2384PubMedGoogle Scholar
  90. Larschan E, Winston F (2001) The S. cerevisiae SAGA complex functions in vivo as a coactivator for transcriptional activation by Gal4. Genes Dev 15(15):1946–1956PubMedGoogle Scholar
  91. Larsen F, Gundersen G, Lopez R, Prydz H (1992) CpG islands as gene markers in the human genome. Genomics 13(4):1095–1107PubMedGoogle Scholar
  92. Lee MG, Wynder C, Cooch N, Shiekhattar R (2005) An essential role for CoREST in nucleosomal histone 3 lysine 4 demethylation. Nature 437(7057):432–435PubMedGoogle Scholar
  93. Lee JS, Shukla A, Schneider J, Swanson SK, Washburn MP, Florens L et al (2007a) Histone crosstalk between H2B monoubiquitination and H3 methylation mediated by COMPASS. Cell 131(6):1084–1096PubMedGoogle Scholar
  94. Lee MG, Norman J, Shilatifard A, Shiekhattar R (2007b) Physical and functional association of a trimethyl H3K4 demethylase and Ring6a/MBLR, a polycomb-like protein. Cell 128(5):877–887PubMedGoogle Scholar
  95. Lee J, Jang SJ, Benoit N, Hoque MO, Califano JA, Trink B et al (2010) Presence of 5-methylcytosine in CpNpG trinucleotides in the human genome. Genomics 96(2):67–72PubMedGoogle Scholar
  96. Li W, Liu M (2011) Distribution of 5-hydroxymethylcytosine in different human tissues. J Nucleic Acids 2011:870726PubMedGoogle Scholar
  97. Li B, Howe L, Anderson S, Yates JR 3rd, Workman JL (2003) The Set2 histone methyltransferase functions through the phosphorylated carboxyl-terminal domain of RNA polymerase II. J Biol Chem 278(11):8897–8903PubMedGoogle Scholar
  98. Li B, Carey M, Workman JL (2007a) The role of chromatin during transcription. Cell 128(4):707–719PubMedGoogle Scholar
  99. Li B, Gogol M, Carey M, Lee D, Seidel C, Workman JL (2007b) Combined action of PHD and chromo domains directs the Rpd3S HDAC to transcribed chromatin. Science (New York, NY) 316(5827):1050–1054Google Scholar
  100. Lister R, Pelizzola M, Dowen RH, Hawkins RD, Hon G, Tonti-Filippini J et al (2009) Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 462(7271):315–322PubMedGoogle Scholar
  101. Liu X, Tesfai J, Evrard YA, Dent SY, Martinez E (2003) c-myc transformation domain recruits the human STAGA complex and requires TRRAP and GCN5 acetylase activity for transcription activation. J Biol Chem 278(22):20405–20412PubMedGoogle Scholar
  102. 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(6648):251–260PubMedGoogle Scholar
  103. Margueron R, Reinberg D (2011) The polycomb complex PRC2 and its mark in life. Nature 469(7330):343–349PubMedGoogle Scholar
  104. Margueron R, Justin N, Ohno K, Sharpe ML, Son J, Drury WJ 3rd et al (2009) Role of the polycomb protein EED in the propagation of repressive histone marks. Nature 461(7265):762–767PubMedGoogle Scholar
  105. Martin C, Zhang Y (2005) The diverse functions of histone lysine methylation. Nat Rev Mol Cell Biol 6(11):838–849PubMedGoogle Scholar
  106. Martinez E, Kundu TK, Fu J, Roeder RG (1998) A human SPT3-TAFII31-GCN5-L acetylase complex distinct from transcription factor IID. J Biol Chem 273(37):23781–23785PubMedGoogle Scholar
  107. Mateescu B, Bourachot B, Rachez C, Ogryzko V, Muchardt C (2008) Regulation of an inducible promoter by an HP1beta-HP1gamma switch. EMBO Rep 9(3):267–272PubMedGoogle Scholar
  108. McMahon SB, Wood MA, Cole MD (2000) The essential cofactor TRRAP recruits the histone acetyltransferase hGCN5 to c-myc. Mol Cell Biol 20(2):556–562PubMedGoogle Scholar
  109. Metzger E, Wissmann M, Yin N, Muller JM, Schneider R, Peters AH et al (2005) LSD1 demethylates repressive histone marks to promote androgen-receptor-dependent transcription. Nature 437(7057):436–439PubMedGoogle Scholar
  110. Miao F, Smith DD, Zhang L, Min A, Feng W, Natarajan R (2008) Lymphocytes from patients with type 1 diabetes display a distinct profile of chromatin histone H3 lysine 9 dimethylation: an epigenetic study in diabetes. Diabetes 57(12):3189–3198PubMedGoogle Scholar
  111. Mikkelsen TS, Ku M, Jaffe DB, Issac B, Lieberman E, Giannoukos G et al (2007) Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 448(7153):553–560PubMedGoogle Scholar
  112. Nagy Z, Tora L (2007) Distinct GCN5/PCAF-containing complexes function as co-activators and are involved in transcription factor and global histone acetylation. Oncogene 26(37):5341–5357PubMedGoogle Scholar
  113. Nan X, Ng HH, Johnson CA, Laherty CD, Turner BM, Eisenman RN et al (1998) Transcriptional repression by the methyl-CpG-binding protein MeCP2 involves a histone deacetylase complex. Nature 393(6683):386–389PubMedGoogle Scholar
  114. Nekrasov M, Klymenko T, Fraterman S, Papp B, Oktaba K, Kocher T et al (2007) Pcl-PRC2 is needed to generate high levels of H3-K27 trimethylation at polycomb target genes. EMBO J 26(18):4078–4088PubMedGoogle Scholar
  115. Ng HH, Robert F, Young RA, Struhl K (2003) Targeted recruitment of Set1 histone methylase by elongating Pol II provides a localized mark and memory of recent transcriptional activity. Mol Cell 11(3):709–719PubMedGoogle Scholar
  116. Ogryzko VV, Kotani T, Zhang X, Schiltz RL, Howard T, Yang XJ et al (1998) Histone-like TAFs within the PCAF histone acetylase complex. Cell 94(1):35–44PubMedGoogle Scholar
  117. Okada Y, Feng Q, Lin Y, Jiang Q, Li Y, Coffield VM et al (2005) hDOT1L links histone methylation to leukemogenesis. Cell 121(2):167–178PubMedGoogle Scholar
  118. Okano M, Bell DW, Haber DA, Li E (1999) DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development. Cell 99(3):247–257PubMedGoogle Scholar
  119. Ordovas JM, Smith CE (2010) Epigenetics and cardiovascular disease. Nat Rev Cardiol 7(9):510–519PubMedGoogle Scholar
  120. Phatnani HP, Greenleaf AL (2006) Phosphorylation and functions of the RNA polymerase II CTD. Genes Dev 20(21):2922–2936PubMedGoogle Scholar
  121. Pokholok DK, Harbison CT, Levine S, Cole M, Hannett NM, Lee TI et al (2005) Genome-wide map of nucleosome acetylation and methylation in yeast. Cell 122(4):517–527PubMedGoogle Scholar
  122. Portela A, Esteller M (2010) Epigenetic modifications and human disease. Nat Biotechnol 28(10):1057–1068PubMedGoogle Scholar
  123. Pray-Grant MG, Daniel JA, Schieltz D, Yates JR 3rd, Grant PA (2005) Chd1 chromodomain links histone H3 methylation with SAGA- and SLIK-dependent acetylation. Nature 433(7024):434–438PubMedGoogle Scholar
  124. Prokhortchouk E, Defossez PA (2008) The cell biology of DNA methylation in mammals. Biochimica Et Biophysica Acta 1783(11):2167–2173PubMedGoogle Scholar
  125. Qiu H, Hu C, Hinnebusch AG (2009) Phosphorylation of the Pol II CTD by KIN28 enhances BUR1/BUR2 recruitment and Ser2 CTD phosphorylation near promoters. Mol Cell 33(6):752–762PubMedGoogle Scholar
  126. Rand E, Ben-Porath I, Keshet I, Cedar H (2004) CTCF elements direct allele-specific undermethylation at the imprinted H19 locus. Curr Biol (CB) 14(11):1007–1012Google Scholar
  127. Reeves WM, Hahn S (2005) Targets of the Gal4 transcription activator in functional transcription complexes. Mol Cell Biol 25(20):9092–9102PubMedGoogle Scholar
  128. Reik W, Lewis A (2005) Co-evolution of X-chromosome inactivation and imprinting in mammals. Nat Rev Genet 6(5):403–410PubMedGoogle Scholar
  129. Rice JC, Briggs SD, Ueberheide B, Barber CM, Shabanowitz J, Hunt DF et al (2003) Histone methyltransferases direct different degrees of methylation to define distinct chromatin domains. Mol Cell 12(6):1591–1598PubMedGoogle Scholar
  130. Rinn JL, Kertesz M, Wang JK, Squazzo SL, Xu X, Brugmann SA et al (2007) Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell 129(7):1311–1323PubMedGoogle Scholar
  131. Rosenfeld JA, Wang Z, Schones DE, Zhao K, DeSalle R, Zhang MQ (2009) Determination of enriched histone modifications in non-genic portions of the human genome. BMC Genomics 10:143PubMedGoogle Scholar
  132. Santos-Rosa H, Schneider R, Bannister AJ, Sherriff J, Bernstein BE, Emre NC et al (2002) Active genes are tri-methylated at K4 of histone H3. Nature 419(6905):407–411PubMedGoogle Scholar
  133. Santos-Rosa H, Kirmizis A, Nelson C, Bartke T, Saksouk N, Cote J et al (2009) Histone H3 tail clipping regulates gene expression. Nat Struct Mol Biol 16(1):17–22PubMedGoogle Scholar
  134. 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 USA 103(5):1412–1417PubMedGoogle Scholar
  135. Scarano E, Iaccarino M, Grippo P, Parisi E (1967) The heterogeneity of thymine methyl group origin in DNA pyrimidine isostichs of developing sea urchin embryos. Proc Natl Acad Sci USA 57(5):1394–1400PubMedGoogle Scholar
  136. Schotta G, Lachner M, Sarma K, Ebert A, Sengupta R, Reuter G et al (2004) A silencing pathway to induce H3-K9 and H4-K20 trimethylation at constitutive heterochromatin. Genes Dev 18(11):1251–1262PubMedGoogle Scholar
  137. Shi Y, Whetstine JR (2007) Dynamic regulation of histone lysine methylation by demethylases. Mol Cell 25(1):1–14PubMedGoogle Scholar
  138. Shi Y, Lan F, Matson C, Mulligan P, Whetstine JR, Cole PA et al (2004) Histone demethylation mediated by the nuclear amine oxidase homolog LSD1. Cell 119(7):941–953PubMedGoogle Scholar
  139. Shi YJ, Matson C, Lan F, Iwase S, Baba T, Shi Y (2005) Regulation of LSD1 histone demethylase activity by its associated factors. Mol Cell 19(6):857–864PubMedGoogle Scholar
  140. Shi X, Hong T, Walter KL, Ewalt M, Michishita E, Hung T et al (2006) ING2 PHD domain links histone H3 lysine 4 methylation to active gene repression. Nature 442(7098):96–99PubMedGoogle Scholar
  141. Shiio Y, Eisenman RN (2003) Histone sumoylation is associated with transcriptional repression. Proc Natl Acad Sci USA 100(23):13225–13230PubMedGoogle Scholar
  142. Shogren-Knaak M, Ishii H, Sun JM, Pazin MJ, Davie JR, Peterson CL (2006) Histone H4-K16 acetylation controls chromatin structure and protein interactions. Science (New York, NY) 311(5762):844–847Google Scholar
  143. Simic R, Lindstrom DL, Tran HG, Roinick KL, Costa PJ, Johnson AD et al (2003) Chromatin remodeling protein Chd1 interacts with transcription elongation factors and localizes to transcribed genes. EMBO J 22(8):1846–1856PubMedGoogle Scholar
  144. Simon JA, Kingston RE (2009) Mechanisms of polycomb gene silencing: knowns and unknowns. Nat Rev Mol Cell Biol 10(10):697–708PubMedGoogle Scholar
  145. Sterner DE, Berger SL (2000) Acetylation of histones and transcription-related factors. Microbiol Mol Biol Rev (MMBR) 64(2):435–459Google Scholar
  146. Strahl BD, Allis CD (2000) The language of covalent histone modifications. Nature 403(6765):41–45PubMedGoogle Scholar
  147. Straussman R, Nejman D, Roberts D, Steinfeld I, Blum B, Benvenisty N et al (2009) Developmental programming of CpG island methylation profiles in the human genome. Nat Struct Mol Biol 16(5):564–571PubMedGoogle Scholar
  148. Swartz MN, Trautner TA, Kornberg A (1962) Enzymatic synthesis of deoxyribonucleic acid. XI. Further studies on nearest neighbor base sequences in deoxyribonucleic acids. J Biol Chem 237:1961–1967PubMedGoogle Scholar
  149. Szabo P, Tang SH, Rentsendorj A, Pfeifer GP, Mann JR (2000) Maternal-specific footprints at putative CTCF sites in the H19 imprinting control region give evidence for insulator function. Curr Biol (CB) 10(10):607–610Google Scholar
  150. Tahiliani M, Koh KP, Shen Y, Pastor WA, Bandukwala H, Brudno Y et al (2009) Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science (New York, NY) 324(5929):930–935Google Scholar
  151. Takai D, Jones PA (2002) Comprehensive analysis of CpG islands in human chromosomes 21 and 22. Proc Natl Acad Sci USA 99(6):3740–3745PubMedGoogle Scholar
  152. Tsukada Y, Fang J, Erdjument-Bromage H, Warren ME, Borchers CH, Tempst P et al (2006) Histone demethylation by a family of JmjC domain-containing proteins. Nature 439(7078):811–816PubMedGoogle Scholar
  153. Turner BM, Birley AJ, Lavender J (1992) Histone H4 isoforms acetylated at specific lysine residues define individual chromosomes and chromatin domains in drosophila polytene nuclei. Cell 69(2):375–384PubMedGoogle Scholar
  154. Vakoc CR, Mandat SA, Olenchock BA, Blobel GA (2005) Histone H3 lysine 9 methylation and HP1gamma are associated with transcription elongation through mammalian chromatin. Mol Cell 19(3):381–391PubMedGoogle Scholar
  155. Vakoc CR, Sachdeva MM, Wang H, Blobel GA (2006) Profile of histone lysine methylation across transcribed mammalian chromatin. Mol Cell Biol 26(24):9185–9195PubMedGoogle Scholar
  156. Valinluck V, Sowers LC (2007) Endogenous cytosine damage products alter the site selectivity of human DNA maintenance methyltransferase DNMT1. Cancer Res 67(3):946–950PubMedGoogle Scholar
  157. Valinluck V, Tsai HH, Rogstad DK, Burdzy A, Bird A, Sowers LC (2004) Oxidative damage to methyl-CpG sequences inhibits the binding of the methyl-CpG binding domain (MBD) of methyl-CpG binding protein 2 (MeCP2). Nucleic Acids Res 32(14):4100–4108PubMedGoogle Scholar
  158. van Leeuwen F, Gafken PR, Gottschling DE (2002) Dot1p modulates silencing in yeast by methylation of the nucleosome core. Cell 109(6):745–756PubMedGoogle Scholar
  159. Vettese-Dadey M, Grant PA, Hebbes TR, Crane-Robinson C, Allis CD, Workman JL (1996) Acetylation of histone H4 plays a primary role in enhancing transcription factor binding to nucleosomal DNA in vitro. EMBO J 15(10):2508–2518PubMedGoogle Scholar
  160. Waddington CH (1957) The strategy of the genes; a discussion of some aspects of theoretical biology. Allen & Unwin, LondonGoogle Scholar
  161. Walter J (2011) An epigenetic tet a tet with pluripotency. Cell Stem Cell 8(2):121–122PubMedGoogle Scholar
  162. Wang S, Robertson GP, Zhu J (2004a) A novel human homologue of drosophila polycomblike gene is up-regulated in multiple cancers. Gene 343(1):69–78PubMedGoogle Scholar
  163. Wang Y, Wysocka J, Sayegh J, Lee YH, Perlin JR, Leonelli L et al (2004b) Human PAD4 regulates histone arginine methylation levels via demethylimination. Science (New York, NY) 306(5694):279–283Google Scholar
  164. Wang YA, Kamarova Y, Shen KC, Jiang Z, Hahn MJ, Wang Y et al (2005) DNA methyltransferase-3a interacts with p53 and represses p53-mediated gene expression. Cancer Biol Ther 4(10):1138–1143PubMedGoogle Scholar
  165. Wang Z, Zang C, Rosenfeld JA, Schones DE, Barski A, Cuddapah S et al (2008) Combinatorial patterns of histone acetylations and methylations in the human genome. Nat Genet 40(7):897–903PubMedGoogle Scholar
  166. Wang Y, Zhang H, Chen Y, Sun Y, Yang F, Yu W et al (2009) LSD1 is a subunit of the NuRD complex and targets the metastasis programs in breast cancer. Cell 138(4):660–672PubMedGoogle Scholar
  167. Warren RA (1980) Modified bases in bacteriophage DNAs. Annu Rev Microbiol 34:137–158PubMedGoogle Scholar
  168. Weber M, Davies JJ, Wittig D, Oakeley EJ, Haase M, Lam WL et al (2005) Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells. Nat Genet 37(8):853–862PubMedGoogle Scholar
  169. Whetstine JR, Nottke A, Lan F, Huarte M, Smolikov S, Chen Z et al (2006) Reversal of histone lysine trimethylation by the JMJD2 family of histone demethylases. Cell 125(3):467–481PubMedGoogle Scholar
  170. Wood A, Schneider J, Dover J, Johnston M, Shilatifard A (2003) The Paf1 complex is essential for histone monoubiquitination by the Rad6-Bre1 complex, which signals for histone methylation by COMPASS and Dot1p. J Biol Chem 278(37):34739–34742PubMedGoogle Scholar
  171. Workman JL, Kingston RE (1998) Alteration of nucleosome structure as a mechanism of transcriptional regulation. Annu Rev Biochem 67:545–579PubMedGoogle Scholar
  172. Wossidlo M, Nakamura T, Lepikhov K, Marques CJ, Zakhartchenko V, Boiani M et al (2011) 5-Hydroxymethylcytosine in the mammalian zygote is linked with epigenetic reprogramming. Nat Commun 2:241PubMedGoogle Scholar
  173. Wyatt GR, Cohen SS (1952) A new pyrimidine base from bacteriophage nucleic acids. Nature 170(4338):1072–1073PubMedGoogle Scholar
  174. Wysocka J, Swigut T, Milne TA, Dou Y, Zhang X, Burlingame AL et al (2005) WDR5 associates with histone H3 methylated at K4 and is essential for H3 K4 methylation and vertebrate development. Cell 121(6):859–872PubMedGoogle Scholar
  175. Xiao T, Hall H, Kizer KO, Shibata Y, Hall MC, Borchers CH et al (2003) Phosphorylation of RNA polymerase II CTD regulates H3 methylation in yeast. Genes Dev 17(5):654–663PubMedGoogle Scholar
  176. Yamane K, Toumazou C, Tsukada Y, Erdjument-Bromage H, Tempst P, Wong J et al (2006) JHDM2A, a JmjC-containing H3K9 demethylase, facilitates transcription activation by androgen receptor. Cell 125(3):483–495PubMedGoogle Scholar
  177. Yamane K, Tateishi K, Klose RJ, Fang J, Fabrizio LA, Erdjument-Bromage H et al (2007) PLU-1 is an H3K4 demethylase involved in transcriptional repression and breast cancer cell proliferation. Mol Cell 25(6):801–812PubMedGoogle Scholar
  178. Yang XJ, Seto E (2007) HATs and HDACs: from structure, function and regulation to novel strategies for therapy and prevention. Oncogene 26(37):5310–5318PubMedGoogle Scholar
  179. Yang XJ, Seto E (2008) The Rpd3/Hda1 family of lysine deacetylases: from bacteria and yeast to mice and men. Nat Rev Mol Cell Biol 9(3):206–218PubMedGoogle Scholar
  180. Yang Y, Lu Y, Espejo A, Wu J, Xu W, Liang S et al (2010) TDRD3 is an effector molecule for arginine-methylated histone marks. Mol Cell 40(6):1016–1023PubMedGoogle Scholar
  181. Yoder JA, Bestor TH (1998) A candidate mammalian DNA methyltransferase related to pmt1p of fission yeast. Hum Mol Genet 7(2):279–284PubMedGoogle Scholar
  182. Zeng L, Zhang Q, Li S, Plotnikov AN, Walsh MJ, Zhou MM (2010) Mechanism and regulation of acetylated histone binding by the tandem PHD finger of DPF3b. Nature 466(7303):258–262PubMedGoogle Scholar
  183. Zhang Y, Reinberg D (2001) Transcription regulation by histone methylation: interplay between different covalent modifications of the core histone tails. Genes Dev 15(18):2343–2360PubMedGoogle Scholar
  184. Zhang X, Yazaki J, Sundaresan A, Cokus S, Chan SW, Chen H et al (2006) Genome-wide high-resolution mapping and functional analysis of DNA methylation in arabidopsis. Cell 126(6):1189–1201PubMedGoogle Scholar
  185. Zhao J, Sun BK, Erwin JA, Song JJ, Lee JT (2008) Polycomb proteins targeted by a short repeat RNA to the mouse X chromosome. Science (New York, NY) 322(5902):750–756Google Scholar
  186. Zhao Q, Rank G, Tan YT, Li H, Moritz RL, Simpson RJ et al (2009) PRMT5-mediated methylation of histone H4R3 recruits DNMT3A, coupling histone and DNA methylation in gene silencing. Nat Struct Mol Biol 16(3):304–311PubMedGoogle Scholar
  187. Zheng S, Wyrick JJ, Reese JC (2010) Novel trans-tail regulation of H2B ubiquitylation and H3K4 methylation by the N terminus of histone H2A. Mol Cell Biol 30(14):3635–3645PubMedGoogle Scholar
  188. Zhu B, Zheng Y, Pham AD, Mandal SS, Erdjument-Bromage H, Tempst P et al (2005) Monoubiquitination of human histone H2B: the factors involved and their roles in HOX gene regulation. Mol Cell 20(4):601–611PubMedGoogle Scholar
  189. Zollman S, Godt D, Prive GG, Couderc JL, Laski FA (1994) The BTB domain, found primarily in zinc finger proteins, defines an evolutionarily conserved family that includes several developmentally regulated genes in drosophila. Proc Natl Acad Sci USA 91(22):10717–10721PubMedGoogle Scholar

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© Springer Science+Business Media Dordrecht 2013

Authors and Affiliations

  1. 1.Department of Biochemistry and Molecular GeneticsUniversity of Virginia School of MedicineCharlottesvilleUSA

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