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Epigenetic Regulation

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Patho-Epigenetics of Infectious Disease

Part of the book series: Advances in Experimental Medicine and Biology ((AEMB,volume 879))

Abstract

Some of the key epigenetic regulatory mechanisms appeared early during evolution, and the acquisition of novel epigenetic regulators apparently facilitated certain evolutionary transitions. In this short review we focus mainly on the major epigenetic mechanisms that control chromatin structure and accessibility in mammalian cells. The enzymes methylating CpG dinucleotides and those involved in the active demethylation of 5-metylcytosine (5mC) are outlined together with the members of the methyl binding protein (MBP) family that bind to and “interpret” the 5mC mark. The enzymes involved in reversible, covalent modifications of core histone proteins that affect chromatin structure are also described briefly. Proteins that build up Polycomb group (PcG) and Trithorax group (TrxG) protein complexes may also modify histones. By establishing heritable chromatin states, PcG and TrxG complexes contribute – similarly to cytosine methylation – to the transmission of cell type-specific gene expression patterns from cell generation to cell generation. Novel players involved in epigenetic regulation, including variant histones, pioneer transcription factors, long noncoding RNA molecules and the regulators of long-distance chromatin interactions are introduced as well, followed by the characterization of various chromatin types.

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References

  • Aoto T, Saitoh N, Sakamoto Y, Watanabe S, Nakao M (2008) Polycomb group protein-associated chromatin is reproduced in post-mitotic G1 phase and is required for S phase progression. J Biol Chem 283:18905–18915

    Article  CAS  PubMed  Google Scholar 

  • Araujo FD, Croteau S, Slack AD, Milutinovic S, Bigey P, Price GB, Zannis-Hadjopoulos M, Szyf M (2001) The DNMT1 target recognition domain resides in the N terminus. J Biol Chem 276:6930–6936

    Article  CAS  PubMed  Google Scholar 

  • Aravind L, Abhiman S, Iyer LM (2011) Natural history of the eukaryotic chromatin protein methylation system. Prog Mol Biol Transl Sci 101:105–176

    Article  CAS  PubMed  Google Scholar 

  • Arope S, Harraghy N, Pjanic M, Mermod N (2013) Molecular characterization of a human matrix attachment region epigenetic regulator. PLoS One 8:e79262

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Bagui TK, Sharma SS, Ma L, Pledger WJ (2013) Proliferative status regulates HDAC11 mRNA abundance in nontransformed fibroblasts. Cell Cycle 12:3433–3441

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bannister AJ, Kouzarides T (2011) Regulation of chromatin by histone modifications. Cell Res 21:381–395

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bassett SA, Barnett MP (2014) The role of dietary histone deacetylases (HDACs) inhibitors in health and disease. Nutrients 6:4273–4301

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Baymaz HI, Fournier A, Laget S, Ji Z, Jansen PW, Smits AH, Ferry L, Mensinga A, Poser I, Sharrocks A, Defossez PA, Vermeulen M (2014) MBD5 and MBD6 interact with the human PR-DUB complex through their methyl-CpG-binding domain. Proteomics 14:2179–2189

    Article  CAS  PubMed  Google Scholar 

  • Bedford MT (2007) Arginine methylation at a glance. J Cell Sci 120:4243–4246

    Article  CAS  PubMed  Google Scholar 

  • Begum NA, Stanlie A, Nakata M, Akiyama H, Honjo T (2012) The histone chaperone Spt6 is required for activation-induced cytidine deaminase target determination through H3K4me3 regulation. J Biol Chem 287:32415–32429

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bell SD, Botting CH, Wardleworth BN, Jackson SP, White MF (2002) The interaction of Alba, a conserved archaeal chromatin protein, with Sir2 and its regulation by acetylation. Science 296:148–151

    Article  CAS  PubMed  Google Scholar 

  • Bestor TH (2000) The DNA methyltransferases of mammals. Hum Mol Genet 9:2395–2402

    Article  CAS  PubMed  Google Scholar 

  • Bird A (2002) DNA methylation patterns and epigenetic memory. Genes Dev 16:6–21

    Article  CAS  PubMed  Google Scholar 

  • Blobel GA, Kadauke S, Wang E, Lau AW, Zuber J, Chou MM, Vakoc CR (2009) A reconfigured pattern of MLL occupancy within mitotic chromatin promotes rapid transcriptional reactivation following mitotic exit. Mol Cell 36:970–983

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Branco MR, Ficz G, Reik W (2012) Uncovering the role of 5-hydroxymethylcytosine in the epigenome. Nat Rev Genet 13:7–13

    CAS  Google Scholar 

  • Burgess RJ, Zhang Z (2013) Histone chaperones in nucleosome assembly and human disease. Nat Struct Mol Biol 20:14–22

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Burke LJ, Zhang R, Bartkuhn M, Tiwari VK, Tavoosidana G, Kurukuti S, Weth C, Leers J, Galjart N, Ohlsson R, Renkawitz R (2005) CTCF binding and higher order chromatin structure of the H19 locus are maintained in mitotic chromatin. EMBO J 24:3291–3300

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cao J, Yan Q (2012) Histone ubiquitination and deubiquitination in transcription, DNA damage response, and cancer. Front Oncol 2:26

    Article  PubMed  PubMed Central  Google Scholar 

  • Cao R, Wang L, Wang H, Xia L, Erdjument-Bromage H, Tempst P, Jones RS, Zhang Y (2002) Role of histone H3 lysine 27 methylation in Polycomb-group silencing. Science 298:1039–1043

    Article  CAS  PubMed  Google Scholar 

  • Caravaca JM, Donahue G, Becker JS, He X, Vinson C, Zaret KS (2013) Bookmarking by specific and nonspecific binding of FoxA1 pioneer factor to mitotic chromosomes. Genes Dev 27:251–260

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Casadesus J, Low DA (2013) Programmed heterogeneity: epigenetic mechanisms in bacteria. J Biol Chem 288:13929–13935

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chang B, Chen Y, Zhao Y, Bruick RK (2007) JMJD6 is a histone arginine demethylase. Science 318:444–447

    Article  CAS  PubMed  Google Scholar 

  • Chen Q, Chen Y, Bian C, Fujiki R, Yu X (2013) TET2 promotes histone O-GlcNAcylation during gene transcription. Nature 493:561–564

    Article  CAS  PubMed  Google Scholar 

  • Cheutin T, Cavalli G (2014) Polycomb silencing: from linear chromatin domains to 3D chromosome folding. Curr Opin Genet Dev 25:30–37

    Article  CAS  PubMed  Google Scholar 

  • Chia N, Wang L, Lu X, Senut MC, Brenner C, Ruden DM (2011) Hypothesis: environmental regulation of 5-hydroxymethylcytosine by oxidative stress. Epigenetics 6:853–856

    Article  PubMed  CAS  Google Scholar 

  • Choi NM, Feeney AJ (2014) CTCF and ncRNA regulate the three-dimensional structure of antigen receptor loci to facilitate V(D)J recombination. Front Immunol 5:49

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Ciabrelli F, Cavalli G (2015) Chromatin-driven behavior of topologically associating domains. J Mol Biol 427(3):608–625

    Google Scholar 

  • Cloos PA, Christensen J, Agger K, Helin K (2008) Erasing the methyl mark: histone demethylases at the center of cellular differentiation and disease. Genes Dev 22:1115–1140

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Coyne RS, Lhuillier-Akakpo M, Duharcourt S (2012) RNA-guided DNA rearrangements in ciliates: is the best genome defence a good offence? Biol Cell 104:309–325

    Article  CAS  PubMed  Google Scholar 

  • Cubonova L, Sandman K, Hallam SJ, Delong EF, Reeve JN (2005) Histones in crenarchaea. J Bacteriol 187:5482–5485

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cuthbert GL, Daujat S, Snowden AW, Erdjument-Bromage H, Hagiwara T, Yamada M, Schneider R, Gregory PD, Tempst P, Bannister AJ, Kouzarides T (2004) Histone deimination antagonizes arginine methylation. Cell 118:545–553

    Article  CAS  PubMed  Google Scholar 

  • De Laat W, Grosveld F (2003) Spatial organization of gene expression: the active chromatin hub. Chromosome Res 11:447–459

    Article  PubMed  Google Scholar 

  • Defossez PA (2013) Ceci n’est pas une DNMT: recently discovered functions of DNMT2 and their relation to methyltransferase activity Comment on doi 10.1002/bies.201300088. Bioessays 35:1024

    Article  CAS  PubMed  Google Scholar 

  • Dehennaut V, Leprince D, Lefebvre T (2014) O-GlcNAcylation, an epigenetic mark. Focus on the histone code, TET family proteins, and polycomb group proteins. Front Endocrinol (Lausanne) 5:155

    Google Scholar 

  • Del Rizzo PA, Trievel RC (2011) Substrate and product specificities of SET domain methyltransferases. Epigenetics 6:1059–1067

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Deplus R, Delatte B, Schwinn MK, Defrance M, Mendez J, Murphy N, Dawson MA, Volkmar M, Putmans P, Calonne E, Shih AH, Levine RL, Bernard O, Mercher T, Solary E, Urh M, Daniels DL, Fuks F (2013) TET2 and TET3 regulate GlcNAcylation and H3K4 methylation through OGT and SET1/COMPASS. EMBO J 32:645–655

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Di Lorenzo A, Bedford MT (2011) Histone arginine methylation. FEBS Lett 585:2024–2031

    Article  PubMed  CAS  Google Scholar 

  • Dillon SC, Zhang X, Trievel RC, Cheng X (2005) The SET-domain protein superfamily: protein lysine methyltransferases. Genome Biol 6:227

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Doerfler W (2012) The impact of foreign DNA integration on tumor biology and evolution via epigenetic alterations. In: Minarovits J, Niller HH (eds) Patho-epigenetics of disease. Springer, New York, pp 14–378

    Google Scholar 

  • Eskeland R, Leeb M, Grimes GR, Kress C, Boyle S, Sproul D, Gilbert N, Fan Y, Skoultchi AI, Wutz A, Bickmore WA (2010) Ring1B compacts chromatin structure and represses gene expression independent of histone ubiquitination. Mol Cell 38:452–464

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ferrari KJ, Scelfo A, Jammula S, Cuomo A, Barozzi I, Stutzer A, Fischle W, Bonaldi T, Pasini D (2014) Polycomb-dependent H3K27me1 and H3K27me2 regulate active transcription and enhancer fidelity. Mol Cell 53:49–62

    Article  CAS  PubMed  Google Scholar 

  • Fisk JC, Read LK (2011) Protein arginine methylation in parasitic protozoa. Eukaryot Cell 10:1013–1022

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Follmer NE, Wani AH, Francis NJ (2012) A polycomb group protein is retained at specific sites on chromatin in mitosis. PLoS Genet 8:e1003135

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Fonseca JP, Steffen PA, Muller S, Lu J, Sawicka A, Seiser C, Ringrose L (2012) In vivo Polycomb kinetics and mitotic chromatin binding distinguish stem cells from differentiated cells. Genes Dev 26:857–871

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Francis NJ, Kingston RE, Woodcock CL (2004) Chromatin compaction by a polycomb group protein complex. Science 306:1574–1577

    Article  CAS  PubMed  Google Scholar 

  • Frangini A, Sjoberg M, Roman-Trufero M, Dharmalingam G, Haberle V, Bartke T, Lenhard B, Malumbres M, Vidal M, Dillon N (2013) The aurora B kinase and the polycomb protein ring1B combine to regulate active promoters in quiescent lymphocytes. Mol Cell 51:647–661

    Article  CAS  PubMed  Google Scholar 

  • Free A, Wakefield RI, Smith BO, Dryden DT, Barlow PN, Bird AP (2001) DNA recognition by the methyl-CpG binding domain of MeCP2. J Biol Chem 276:3353–3360

    Article  CAS  PubMed  Google Scholar 

  • Fuks F, Hurd PJ, Wolf D, Nan X, Bird AP, Kouzarides T (2003) The methyl-CpG-binding protein MeCP2 links DNA methylation to histone methylation. J Biol Chem 278:4035–4040

    Article  CAS  PubMed  Google Scholar 

  • Gao Z, Zhang J, Bonasio R, Strino F, Sawai A, Parisi F, Kluger Y, Reinberg D (2012) PCGF homologs, CBX proteins, and RYBP define functionally distinct PRC1 family complexes. Mol Cell 45:344–356

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gareau JR, Lima CD (2010) The SUMO pathway: emerging mechanisms that shape specificity, conjugation and recognition. Nat Rev Mol Cell Biol 11:861–871

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gatto S, D’Esposito M, Matarazzo MR (2012) The role of DNMT3B mutations in the pathogenesis of ICF syndrome. In: Minarovits J, Niller HH (eds) Patho-epigenetics of disease. Springer, New York, pp 15–41

    Chapter  Google Scholar 

  • Goll MG, Kirpekar F, Maggert KA, Yoder JA, Hsieh CL, Zhang X, Golic KG, Jacobsen SE, Bestor TH (2006) Methylation of tRNAAsp by the DNA methyltransferase homolog Dnmt2. Science 311:395–398

    Article  CAS  PubMed  Google Scholar 

  • Goto H, Yasui Y, Nigg EA, Inagaki M (2002) Aurora-B phosphorylates histone H3 at serine28 with regard to the mitotic chromosome condensation. Genes Cells 7:11–17

    Article  CAS  PubMed  Google Scholar 

  • Gyory I, Minarovits J (2005) Epigenetic regulation of lymphoid specific gene sets. Biochem Cell Biol 83:286–295

    Article  PubMed  Google Scholar 

  • Haberland M, Montgomery RL, Olson EN (2009) The many roles of histone deacetylases in development and physiology: implications for disease and therapy. Nat Rev Genet 10:32–42

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Harmston N, Lenhard B (2013) Chromatin and epigenetic features of long-range gene regulation. Nucleic Acids Res 41:7185–7199

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Harshman SW, Young NL, Parthun MR, Freitas MA (2013) H1 histones: current perspectives and challenges. Nucleic Acids Res 41:9593–9609

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hashimoto H, Horton JR, Zhang X, Bostick M, Jacobsen SE, Cheng X (2008) The SRA domain of UHRF1 flips 5-methylcytosine out of the DNA helix. Nature 455:826–829

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hashimoto H, Vertino PM, Cheng X (2010) Molecular coupling of DNA methylation and histone methylation. Epigenomics 2:657–669

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hendrich B, Tweedie S (2003) The methyl-CpG binding domain and the evolving role of DNA methylation in animals. Trends Genet 19:269–277

    Article  CAS  PubMed  Google Scholar 

  • Hervouet E, Lalier L, Debien E, Cheray M, Geairon A, Rogniaux H, Loussouarn D, Martin SA, Vallette FM, Cartron PF (2010) Disruption of Dnmt1/PCNA/UHRF1 interactions promotes tumorigenesis from human and mice glial cells. PLoS One 5:e11333

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Hervouet E, Nadaradjane A, Gueguen M, Vallette FM, Cartron PF (2012) Kinetics of DNA methylation inheritance by the Dnmt1-including complexes during the cell cycle. Cell Div 7:5

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hill PW, Amouroux R, Hajkova P (2014) DNA demethylation, Tet proteins and 5-hydroxymethylcytosine in epigenetic reprogramming: an emerging complex story. Genomics 104:324–333

    Article  CAS  PubMed  Google Scholar 

  • Hoeijmakers WA, Stunnenberg HG, Bartfai R (2012) Placing the Plasmodium falciparum epigenome on the map. Trends Parasitol 28:486–495

    Article  CAS  PubMed  Google Scholar 

  • Horikoshi M (2013) Histone acetylation: from code to web and router via intrinsically disordered regions. Curr Pharm Des 19:5019–5042

    Article  CAS  PubMed  Google Scholar 

  • Howe FS, Boubriak I, Sale MJ, Nair A, Clynes D, Grijzenhout A, Murray SC, Woloszczuk R, Mellor J (2014) Lysine acetylation controls local protein conformation by influencing proline isomerization. Mol Cell 55:733–744

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Iida T, Suetake I, Tajima S, Morioka H, Ohta S, Obuse C, Tsurimoto T (2002) PCNA clamp facilitates action of DNA cytosine methyltransferase 1 on hemimethylated DNA. Genes Cells 7:997–1007

    Article  CAS  PubMed  Google Scholar 

  • Iyer LM, Tahiliani M, Rao A, Aravind L (2009) Prediction of novel families of enzymes involved in oxidative and other complex modifications of bases in nucleic acids. Cell Cycle 8:1698–1710

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Jeltsch A (2013) Oxygen, epigenetic signaling, and the evolution of early life. Trends Biochem Sci 38:172–176

    Article  CAS  PubMed  Google Scholar 

  • Jenuwein T, Allis CD (2001) Translating the histone code. Science 293:1074–1080

    Article  CAS  PubMed  Google Scholar 

  • Jin C, Zang C, Wei G, Cui K, Peng W, Zhao K, Felsenfeld G (2009) H3.3/H2A.Z double variant-containing nucleosomes mark ‘nucleosome-free regions’ of active promoters and other regulatory regions. Nat Genet 41:941–945

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Jin B, Li Y, Robertson KD (2011) DNA methylation: superior or subordinate in the epigenetic hierarchy? Genes Cancer 2:607–617

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Jones PA, Liang G (2009) Rethinking how DNA methylation patterns are maintained. Nat Rev Genet 10:805–811

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Josling GA, Selvarajah SA, Petter M, Duffy MF (2012) The role of bromodomain proteins in regulating gene expression. Genes (Basel) 3:320–343

    CAS  Google Scholar 

  • Jurkowski TP, Jeltsch A (2011) On the evolutionary origin of eukaryotic DNA methyltransferases and Dnmt2. PLoS One 6:e28104

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kagey MH, Newman JJ, Bilodeau S, Zhan Y, Orlando DA, Van Berkum NL, Ebmeier CC, Goossens J, Rahl PB, Levine SS, Taatjes DJ, Dekker J, Young RA (2010) Mediator and cohesin connect gene expression and chromatin architecture. Nature 467:430–435

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kaustov L, Ouyang H, Amaya M, Lemak A, Nady N, Duan S, Wasney GA, Li Z, Vedadi M, Schapira M, Min J, Arrowsmith CH (2011) Recognition and specificity determinants of the human cbx chromodomains. J Biol Chem 286:521–529

    Article  CAS  PubMed  Google Scholar 

  • Keller C, Buhler M (2013) Chromatin-associated ncRNA activities. Chromosome Res 21:627–641

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kelly TK, Jones PA (2011) Role of nucleosomes in mitotic bookmarking. Cell Cycle 10:370–371

    Article  CAS  PubMed  Google Scholar 

  • Kelly TK, Miranda TB, Liang G, Berman BP, Lin JC, Tanay A, Jones PA (2010) H2A.Z maintenance during mitosis reveals nucleosome shifting on mitotically silenced genes. Mol Cell 39:901–911

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Khalil AM, Guttman M, Huarte M, Garber M, Raj A, Rivea Morales D, Thomas K, Presser A, Bernstein BE, Van Oudenaarden A, Regev A, Lander ES, Rinn JL (2009) Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc Natl Acad Sci U S A 106:11667–11672

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kim J, Guermah M, McGinty RK, Lee JS, Tang Z, Milne TA, Shilatifard A, Muir TW, Roeder RG (2009) RAD6-Mediated transcription-coupled H2B ubiquitylation directly stimulates H3K4 methylation in human cells. Cell 137:459–471

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kishore SP, Stiller JW, Deitsch KW (2013) Horizontal gene transfer of epigenetic machinery and evolution of parasitism in the malaria parasite Plasmodium falciparum and other apicomplexans. BMC Evol Biol 13:37

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Komura J, Ikehata H, Ono T (2007) Chromatin fine structure of the c-MYC insulator element/DNase I-hypersensitive site I is not preserved during mitosis. Proc Natl Acad Sci U S A 104:15741–15746

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kornberg RD (1974) Chromatin structure: a repeating unit of histones and DNA. Science 184:868–871

    Article  CAS  PubMed  Google Scholar 

  • Kouzarides T (2007) Chromatin modifications and their function. Cell 128:693–705

    Article  CAS  PubMed  Google Scholar 

  • Krauss V, Fassl A, Fiebig P, Patties I, Sass H (2006) The evolution of the histone methyltransferase gene Su(var)3-9 in metazoans includes a fusion with and a re-fission from a functionally unrelated gene. BMC Evol Biol 6:18

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Kumar PP, Bischof O, Purbey PK, Notani D, Urlaub H, Dejean A, Galande S (2007) Functional interaction between PML and SATB1 regulates chromatin-loop architecture and transcription of the MHC class I locus. Nat Cell Biol 9:45–56

    Article  PubMed  CAS  Google Scholar 

  • Labbe RM, Holowatyj A, Yang ZQ (2013) Histone lysine demethylase (KDM) subfamily 4: structures, functions and therapeutic potential. Am J Transl Res 6:1–15

    PubMed  PubMed Central  Google Scholar 

  • Lakshmaiah KC, Jacob LA, Aparna S, Lokanatha D, Saldanha SC (2014) Epigenetic therapy of cancer with histone deacetylase inhibitors. J Cancer Res Ther 10:469–478

    CAS  PubMed  Google Scholar 

  • Lanzuolo C, Lo Sardo F, Orlando V (2012) Concerted epigenetic signatures inheritance at PcG targets through replication. Cell Cycle 11:1296–1300

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Liu HW, Zhang J, Heine GF, Arora M, Gulcin Ozer H, Onti-Srinivasan R, Huang K, Parvin JD (2012) Chromatin modification by SUMO-1 stimulates the promoters of translation machinery genes. Nucleic Acids Res 40:10172–10186

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Long HK, Blackledge NP, Klose RJ (2013) ZF-CxxC domain-containing proteins, CpG islands and the chromatin connection. Biochem Soc Trans 41:727–740

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Luderus ME, De Graaf A, Mattia E, Den Blaauwen JL, Grande MA, De Jong L, Van Driel R (1992) Binding of matrix attachment regions to lamin B1. Cell 70:949–959

    Article  CAS  PubMed  Google Scholar 

  • Mailand N, Bekker-Jensen S, Faustrup H, Melander F, Bartek J, Lukas C, Lukas J (2007) RNF8 ubiquitylates histones at DNA double-strand breaks and promotes assembly of repair proteins. Cell 131:887–900

    Article  CAS  PubMed  Google Scholar 

  • Manzur KL, Zhou MM (2005) An archaeal SET domain protein exhibits distinct lysine methyltransferase activity towards DNA-associated protein MC1-alpha. FEBS Lett 579:3859–3865

    Article  CAS  PubMed  Google Scholar 

  • Margueron R, Reinberg D (2011) The Polycomb complex PRC2 and its mark in life. Nature 469:343–349

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Melnik S, Deng B, Papantonis A, Baboo S, Carr IM, Cook PR (2011) The proteomes of transcription factories containing RNA polymerases I, II or III. Nat Methods 8:963–968

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Miller T, Krogan NJ, Dover J, Erdjument-Bromage H, Tempst P, Johnston M, Greenblatt JF, Shilatifard A (2001) COMPASS: a complex of proteins associated with a trithorax-related SET domain protein. Proc Natl Acad Sci U S A 98:12902–12907

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mousavi K, Zare H, Wang AH, Sartorelli V (2012) Polycomb protein Ezh1 promotes RNA polymerase II elongation. Mol Cell 45:255–262

    Article  CAS  PubMed  Google Scholar 

  • Murnion ME, Adams RR, Callister DM, Allis CD, Earnshaw WC, Swedlow JR (2001) Chromatin-associated protein phosphatase 1 regulates aurora-B and histone H3 phosphorylation. J Biol Chem 276:26656–26665

    Article  CAS  PubMed  Google Scholar 

  • Nan X, Meehan RR, Bird A (1993) Dissection of the methyl-CpG binding domain from the chromosomal protein MeCP2. Nucleic Acids Res 21:4886–4892

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Nan X, Ng HH, Johnson CA, Laherty CD, Turner BM, Eisenman RN, Bird A (1998) Transcriptional repression by the methyl-CpG-binding protein MeCP2 involves a histone deacetylase complex. Nature 393:386–389

    Article  CAS  PubMed  Google Scholar 

  • Nelson CJ, Santos-Rosa H, Kouzarides T (2006) Proline isomerization of histone H3 regulates lysine methylation and gene expression. Cell 126:905–916

    Article  CAS  PubMed  Google Scholar 

  • Nguyen AT, Zhang Y (2011) The diverse functions of Dot1 and H3K79 methylation. Genes Dev 25:1345–1358

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Nie L, Wu HJ, Hsu JM, Chang SS, Labaff AM, Li CW, Wang Y, Hsu JL, Hung MC (2012) Long non-coding RNAs: versatile master regulators of gene expression and crucial players in cancer. Am J Transl Res 4:127–150

    CAS  PubMed  PubMed Central  Google Scholar 

  • Niller HH, Banati F, Ay E, Minarovits J (2012) Microbe-induced epigenetic alterations. In: Minarovits J, Niller HH (eds) Patho-epigenetics of disease. Springer, New York, pp 419–455

    Chapter  Google Scholar 

  • Niu Y, Xia Y, Wang S, Li J, Niu C, Li X, Zhao Y, Xiong H, Li Z, Lou H, Cao Q (2013) A prototypic lysine methyltransferase 4 from archaea with degenerate sequence specificity methylates chromatin proteins Sul7d and Cren7 in different patterns. J Biol Chem 288:13728–13740

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ooi SK, O’Donnell AH, Bestor TH (2009) Mammalian cytosine methylation at a glance. J Cell Sci 122:2787–2791

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Osborne CS (2014) Molecular pathways: transcription factories and chromosomal translocations. Clin Cancer Res 20:296–300

    Article  CAS  PubMed  Google Scholar 

  • Osborne CS, Chakalova L, Brown KE, Carter D, Horton A, Debrand E, Goyenechea B, Mitchell JA, Lopes S, Reik W, Fraser P (2004) Active genes dynamically colocalize to shared sites of ongoing transcription. Nat Genet 36:1065–1071

    Article  CAS  PubMed  Google Scholar 

  • Papantonis A, Cook PR (2013) Transcription factories: genome organization and gene regulation. Chem Rev 113:8683–8705

    Article  CAS  PubMed  Google Scholar 

  • Park SK, Xiang Y, Feng X, Garrard WT (2014) Pronounced cohabitation of active immunoglobulin genes from three different chromosomes in transcription factories during maximal antibody synthesis. Genes Dev 28:1159–1164

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Parry L, Clarke AR (2011) The roles of the methyl-CpG binding proteins in cancer. Genes Cancer 2:618–630

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Petruk S, Sedkov Y, Johnston DM, Hodgson JW, Black KL, Kovermann SK, Beck S, Canaani E, Brock HW, Mazo A (2012) TrxG and PcG proteins but not methylated histones remain associated with DNA through replication. Cell 150:922–933

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Posfai J, Bhagwat AS, Posfai G, Roberts RJ (1989) Predictive motifs derived from cytosine methyltransferases. Nucleic Acids Res 17:2421–2435

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Poulard C, Rambaud J, Hussein N, Corbo L, Le Romancer M (2014) JMJD6 regulates ERalpha methylation on arginine. PLoS One 9:e87982

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Reeve JN (2003) Archaeal chromatin and transcription. Mol Microbiol 48:587–598

    Article  CAS  PubMed  Google Scholar 

  • Richmond TJ, Finch JT, Rushton B, Rhodes D, Klug A (1984) Structure of the nucleosome core particle at 7 A resolution. Nature 311:532–537

    Article  CAS  PubMed  Google Scholar 

  • Rinn JL, Kertesz M, Wang JK, Squazzo SL, Xu X, Brugmann SA, Goodnough LH, Helms JA, Farnham PJ, Segal E, Chang HY (2007) Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell 129:1311–1323

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Robertson KD (2001) DNA methylation, methyltransferases, and cancer. Oncogene 20:3139–3155

    Article  CAS  PubMed  Google Scholar 

  • Rohlf T, Steiner L, Przybilla J, Prohaska S, Binder H, Galle J (2012) Modeling the dynamic epigenome: from histone modifications towards self-organizing chromatin. Epigenomics 4:205–219

    Article  CAS  PubMed  Google Scholar 

  • Roth SY, Denu JM, Allis CD (2001) Histone acetyltransferases. Annu Rev Biochem 70:81–120

    Article  CAS  PubMed  Google Scholar 

  • Rubio ED, Reiss DJ, Welcsh PL, Disteche CM, Filippova GN, Baliga NS, Aebersold R, Ranish JA, Krumm A (2008) CTCF physically links cohesin to chromatin. Proc Natl Acad Sci U S A 105:8309–8314

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sabbattini P, Sjoberg M, Nikic S, Frangini A, Holmqvist PH, Kunowska N, Carroll T, Brookes E, Arthur SJ, Pombo A, Dillon N (2014) An H3K9/S10 methyl-phospho switch modulates Polycomb and Pol II binding at repressed genes during differentiation. Mol Biol Cell 25:904–915

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Sarraf SA, Stancheva I (2004) Methyl-CpG binding protein MBD1 couples histone H3 methylation at lysine 9 by SETDB1 to DNA replication and chromatin assembly. Mol Cell 15:595–605

    Article  CAS  PubMed  Google Scholar 

  • Sawicka A, Seiser C (2012) Histone H3 phosphorylation – a versatile chromatin modification for different occasions. Biochimie 94:2193–2201

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sawicka A, Seiser C (2014) Sensing core histone phosphorylation – a matter of perfect timing. Biochim Biophys Acta 1839:711–718

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Scelfo A, Piunti A, Pasini D (2015) The controversial role of the Polycomb group proteins in transcription and cancer: how much do we not understand Polycomb proteins? FEBS J 282(9):1703–1722

    Google Scholar 

  • Schuettengruber B, Cavalli G (2010) The DUBle life of polycomb complexes. Dev Cell 18:878–880

    Article  CAS  PubMed  Google Scholar 

  • Schuettengruber B, Chourrout D, Vervoort M, Leblanc B, Cavalli G (2007) Genome regulation by polycomb and trithorax proteins. Cell 128:735–745

    Article  CAS  PubMed  Google Scholar 

  • Schwartz YB, Pirrotta V (2007) Polycomb silencing mechanisms and the management of genomic programmes. Nat Rev Genet 8:9–22

    Article  CAS  PubMed  Google Scholar 

  • Shibata Y, Nishiwaki K (2014) Maintenance of cell fates through acetylated histone and the histone variant H2A.z in C. elegans. Worm 3:e29048

    Article  PubMed  PubMed Central  Google Scholar 

  • Shiio Y, Eisenman RN (2003) Histone sumoylation is associated with transcriptional repression. Proc Natl Acad Sci U S A 100:13225–13230

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Shilatifard A (2012) The COMPASS family of histone H3K4 methylases: mechanisms of regulation in development and disease pathogenesis. Annu Rev Biochem 81:65–95

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Simon JA, Kingston RE (2009) Mechanisms of polycomb gene silencing: knowns and unknowns. Nat Rev Mol Cell Biol 10:697–708

    Article  CAS  PubMed  Google Scholar 

  • Simon JA, Kingston RE (2013) Occupying chromatin: Polycomb mechanisms for getting to genomic targets, stopping transcriptional traffic, and staying put. Mol Cell 49:808–824

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sin HS, Barski A, Zhang F, Kartashov AV, Nussenzweig A, Chen J, Andreassen PR, Namekawa SH (2012) RNF8 regulates active epigenetic modifications and escape gene activation from inactive sex chromosomes in post-meiotic spermatids. Genes Dev 26:2737–2748

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Smith ZD, Meissner A (2013) The simplest explanation: passive DNA demethylation in PGCs. EMBO J 32:318–321

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Spada F, Haemmer A, Kuch D, Rothbauer U, Schermelleh L, Kremmer E, Carell T, Langst G, Leonhardt H (2007) DNMT1 but not its interaction with the replication machinery is required for maintenance of DNA methylation in human cells. J Cell Biol 176:565–571

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Steffen PA, Fonseca JP, Ganger C, Dworschak E, Kockmann T, Beisel C, Ringrose L (2013) Quantitative in vivo analysis of chromatin binding of Polycomb and Trithorax group proteins reveals retention of ASH1 on mitotic chromatin. Nucleic Acids Res 41:5235–5250

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Stevenson JS, Liu H (2013) Nucleosome assembly factors CAF-1 and HIR modulate epigenetic switching frequencies in an H3K56 acetylation-associated manner in Candida albicans. Eukaryot Cell 12:591–603

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Strahl BD, Allis CD (2000) The language of covalent histone modifications. Nature 403:41–45

    Article  CAS  PubMed  Google Scholar 

  • Subbanna S, Nagre NN, Shivakumar M, Umapathy NS, Psychoyos D, Basavarajappa BS (2014) Ethanol induced acetylation of histone at G9a exon1 and G9a-mediated histone H3 dimethylation leads to neurodegeneration in neonatal mice. Neuroscience 258:422–432

    Article  CAS  PubMed  Google Scholar 

  • Sugiyama K, Sugiura K, Hara T, Sugimoto K, Shima H, Honda K, Furukawa K, Yamashita S, Urano T (2002) Aurora-B associated protein phosphatases as negative regulators of kinase activation. Oncogene 21:3103–3111

    Article  CAS  PubMed  Google Scholar 

  • Tan M, Luo H, Lee S, Jin F, Yang JS, Montellier E, Buchou T, Cheng Z, Rousseaux S, Rajagopal N, Lu Z, Ye Z, Zhu Q, Wysocka J, Ye Y, Khochbin S, Ren B, Zhao Y (2011) Identification of 67 histone marks and histone lysine crotonylation as a new type of histone modification. Cell 146:1016–1028

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tang CW, Maya-Mendoza A, Martin C, Zeng K, Chen S, Feret D, Wilson SA, Jackson DA (2008) The integrity of a lamin-B1-dependent nucleoskeleton is a fundamental determinant of RNA synthesis in human cells. J Cell Sci 121:1014–1024

    Article  CAS  PubMed  Google Scholar 

  • Tavares L, Dimitrova E, Oxley D, Webster J, Poot R, Demmers J, Bezstarosti K, Taylor S, Ura H, Koide H, Wutz A, Vidal M, Elderkin S, Brockdorff N (2012) RYBP-PRC1 complexes mediate H2A ubiquitylation at polycomb target sites independently of PRC2 and H3K27me3. Cell 148:664–678

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Thomson JP, Skene PJ, Selfridge J, Clouaire T, Guy J, Webb S, Kerr AR, Deaton A, Andrews R, James KD, Turner DJ, Illingworth R, Bird A (2010) CpG islands influence chromatin structure via the CpG-binding protein Cfp1. Nature 464:1082–1086

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tsai MC, Manor O, Wan Y, Mosammaparast N, Wang JK, Lan F, Shi Y, Segal E, Chang HY (2010) Long noncoding RNA as modular scaffold of histone modification complexes. Science 329:689–693

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Van Emburgh BO, Robertson KD (2008) DNA methyltransferases and methyl-CpG binding proteins as multifunctional regulators of chromatin structure and development. In: Trost J (ed) Epigenetics. Caister Academic Press, Norfolk, pp 23–61

    Google Scholar 

  • Vella P, Scelfo A, Jammula S, Chiacchiera F, Williams K, Cuomo A, Roberto A, Christensen J, Bonaldi T, Helin K, Pasini D (2013) Tet proteins connect the O-linked N-acetylglucosamine transferase Ogt to chromatin in embryonic stem cells. Mol Cell 49:645–656

    Article  CAS  PubMed  Google Scholar 

  • Voigt P, Tee WW, Reinberg D (2013) A double take on bivalent promoters. Genes Dev 27:1318–1338

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Volle C, Dalal Y (2014) Histone variants: the tricksters of the chromatin world. Curr Opin Genet Dev 25:8–14, 138

    Article  CAS  PubMed  Google Scholar 

  • Wang H, Wang L, Erdjument-Bromage H, Vidal M, Tempst P, Jones RS, Zhang Y (2004) Role of histone H2A ubiquitination in Polycomb silencing. Nature 431:873–878

    Article  CAS  PubMed  Google Scholar 

  • Wang AH, Zare H, Mousavi K, Wang C, Moravec CE, Sirotkin HI, Ge K, Gutierrez-Cruz G, Sartorelli V (2013) The histone chaperone Spt6 coordinates histone H3K27 demethylation and myogenesis. EMBO J 32:1075–1086

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Wardleworth BN, Russell RJ, Bell SD, Taylor GL, White MF (2002) Structure of Alba: an archaeal chromatin protein modulated by acetylation. EMBO J 21:4654–4662

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Weber CM, Henikoff S (2014) Histone variants: dynamic punctuation in transcription. Genes Dev 28:672–682

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Williams K, Christensen J, Pedersen MT, Johansen JV, Cloos PA, Rappsilber J, Helin K (2011) TET1 and hydroxymethylcytosine in transcription and DNA methylation fidelity. Nature 473:343–348

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Williams K, Christensen J, Helin K (2012) DNA methylation: TET proteins-guardians of CpG islands? EMBO Rep 13:28–35

    Article  CAS  Google Scholar 

  • Wu H, Zhang Y (2011) Tet1 and 5-hydroxymethylation. A genome-wide view in mouse embryonic stem cells. Cell Cycle 10(15):2428–2436

    Google Scholar 

  • Xu C, Bian C, Lam R, Dong A, Min J (2011) The structural basis for selective binding of non-methylated CpG islands by the CFP1 CXXC domain. Nat Commun 2:227

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Xu YM, Du JY, Lau AT (2014) Posttranslational modifications of human histone H3: an update. Proteomics 14:2047–2060

    Article  PubMed  CAS  Google Scholar 

  • Yang XJ (2004) The diverse superfamily of lysine acetyltransferases and their roles in leukemia and other diseases. Nucleic Acids Res 32:959–976

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yang XJ, Chiang CM (2013) Sumoylation in gene regulation, human disease, and therapeutic action. F1000Prime Rep 5:45

    Article  PubMed  PubMed Central  Google Scholar 

  • 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 9:206–218

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yang SH, Sharrocks AD (2004) SUMO promotes HDAC-mediated transcriptional repression. Mol Cell 13:611–617

    Article  CAS  PubMed  Google Scholar 

  • Zaidi SK, Young DW, Montecino M, Van Wijnen AJ, Stein JL, Lian JB, Stein GS (2011) Bookmarking the genome: maintenance of epigenetic information. J Biol Chem 286:18355–18361

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zaret KS, Carroll JS (2011) Pioneer transcription factors: establishing competence for gene expression. Genes Dev 25:2227–2241

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zaret KS, Watts J, Xu J, Wandzioch E, Smale ST, Sekiya T (2008) Pioneer factors, genetic competence, and inductive signaling: programming liver and pancreas progenitors from the endoderm. Cold Spring Harb Symp Quant Biol 73:119–126

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhu Q, Wani AA (2010) Histone modifications: crucial elements for damage response and chromatin restoration. J Cell Physiol 223:283–288

    CAS  PubMed  PubMed Central  Google Scholar 

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Minarovits, J., Banati, F., Szenthe, K., Niller, H.H. (2016). Epigenetic Regulation. In: Minarovits, J., Niller, H. (eds) Patho-Epigenetics of Infectious Disease. Advances in Experimental Medicine and Biology, vol 879. Springer, Cham. https://doi.org/10.1007/978-3-319-24738-0_1

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