You are never alone: crosstalk among epigenetic players
Tóm tắt
Different cell types in a certain organism contain the same genome while running diverse transcription programs. This is controlled by epigenetic information, including DNA modifications, histone modifications, histone variants, non-coding RNAs, and chromatin architectures. Interestingly, recent progresses revealed extensive crosstalks among these epigenetic players. We discuss here how epigenetic players coordinate with each other to maintain epigenetic identities in mammal cells. More exciting researches are expected to expand our understanding regarding the epigenetic regulatory network.
Tài liệu tham khảo
Alabert C, Groth A (2012) Chromatin replication and epigenome maintenance. Nat Rev Mol Cell Biol 13:153–167
Moazed D (2011) Mechanisms for the inheritance of chromatin states. Cell 146:510–518
Zhu B, Reinberg D (2011) Epigenetic inheritance: uncontested? Cell Res 21:435–441
Huang C, Xu M, Zhu B (2013) Epigenetic inheritance mediated by histone lysine methylation: maintaining transcriptional states without the precise restoration of marks? Philos Trans R Soc Lond B Biol Sci 368:20110332
Yuan G, Zhu B (2013) Histone variants and epigenetic inheritance. Biochim Biophys Acta 1819:222–229
Li E, Bestor TH, Jaenisch R (1992) Targeted mutation of the DNA methyltransferase gene results in embryonic lethality. Cell 69:915–926
Okano M, Bell DW, Haber DA, Li E (1999) DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development. Cell 99:247–257
Bird A (2002) DNA methylation patterns and epigenetic memory. Genes Dev 16:6–21
Meissner A, Mikkelsen TS, Gu H et al (2008) Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature 454:766–770
Nan X, Ng HH, Johnson CA et al (1998) Transcriptional repression by the methyl-CpG-binding protein MeCP2 involves a histone deacetylase complex. Nature 393:386–389
Jones PL, Veenstra GJ, Wade PA et al (1998) Methylated DNA and MeCP2 recruit histone deacetylase to repress transcription. Nat Genet 19:187–191
Hendrich B, Bird A (1998) Identification and characterization of a family of mammalian methyl-CpG binding proteins. Mol Cell Biol 18:6538–6547
Lyst MJ, Ekiert R, Ebert DH et al (2013) Rett syndrome mutations abolish the interaction of MeCP2 with the NCoR/SMRT co-repressor. Nat Neurosci 16:898–902
Zhang Y, Ng HH, Erdjument-Bromage H et al (1999) Analysis of the NuRD subunits reveals a histone deacetylase core complex and a connection with DNA methylation. Genes Dev 13:1924–1935
Wade PA, Gegonne A, Jones PL et al (1999) Mi-2 complex couples DNA methylation to chromatin remodelling and histone deacetylation. Nat Genet 23:62–66
Fujita N, Watanabe S, Ichimura T et al (2003) Methyl-CpG binding domain 1 (MBD1) interacts with the Suv39h1-HP1 heterochromatic complex for DNA methylation-based transcriptional repression. J Biol Chem 278:24132–24138
Ooi SKT, Qiu C, Bernstein E et al (2007) DNMT3L connects unmethylated lysine 4 of histone H3 to de novo methylation of DNA. Nature 448:714–717
Otani J, Nankumo T, Arita K et al (2009) Structural basis for recognition of H3K4 methylation status by the DNA methyltransferase 3A ATRX-DNMT3-DNMT3L domain. EMBO Rep 10:1235–1241
Li B-Z, Huang Z, Cui Q-Y et al (2011) Histone tails regulate DNA methylation by allosterically activating de novo methyltransferase. Cell Res 21:1172–1181
Hu J-L, Zhou BO, Zhang R-R et al (2009) The N-terminus of histone H3 is required for de novo DNA methylation in chromatin. Proc Natl Acad Sci USA 106:22187–22192
Jia D, Jurkowska RZ, Zhang X et al (2007) Structure of Dnmt3a bound to Dnmt3L suggests a model for de novo DNA methylation. Nature 449:248–251
Guo X, Wang L, Li J et al (2014) Structural insight into autoinhibition and histone H3-induced activation of DNMT3A. Nature 517:640–644
Zhang Y, Jurkowska R, Soeroes S et al (2010) Chromatin methylation activity of Dnmt3a and Dnmt3a/3L is guided by interaction of the ADD domain with the histone H3 tail. Nucleic Acids Res 38:4246–4253
Okitsu CY, Hsieh C-L (2007) DNA methylation dictates histone H3K4 methylation. Mol Cell Biol 27:2746–2757
Weber M, Hellmann I, Stadler MB et al (2007) Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nat Genet 39:457–466
Epsztejn-Litman S, Feldman N, Abu-Remaileh M et al (2008) De novo DNA methylation promoted by G9a prevents reprogramming of embryonically silenced genes. Nat Struct Mol Biol 15:1176–1183
Leung DC, Dong KB, Maksakova IA et al (2011) Lysine methyltransferase G9a is required for de novo DNA methylation and the establishment, but not the maintenance, of proviral silencing. Proc Natl Acad Sci USA 108:5718–5723
Estève P-O, Chin HG, Smallwood A et al (2006) Direct interaction between DNMT1 and G9a coordinates DNA and histone methylation during replication. Genes Dev 20:3089–3103
Achour M, Jacq X, Rondé P et al (2008) The interaction of the SRA domain of ICBP90 with a novel domain of DNMT1 is involved in the regulation of VEGF gene expression. Oncogene 27:2187–2197
Karagianni P, Amazit L, Qin J, Wong J (2008) ICBP90, a novel methyl K9 H3 binding protein linking protein ubiquitination with heterochromatin formation. Mol Cell Biol 28:705–717
Rothbart SB, Krajewski K, Nady N et al (2012) Association of UHRF1 with methylated H3K9 directs the maintenance of DNA methylation. Nat Struct Mol Biol 19:1155–1160
Viré E, Brenner C, Deplus R et al (2006) The Polycomb group protein EZH2 directly controls DNA methylation. Nature 439:871–874
Wu H, Coskun V, Tao J et al (2010) Dnmt3a-dependent nonpromoter DNA methylation facilitates transcription of neurogenic genes. Science 329:444–448
Lindroth AM, Park YJ, McLean CM et al (2008) Antagonism between DNA and H3K27 methylation at the imprinted Rasgrf1 locus. PLoS Genet 4:e1000145
Mohn F, Weber M, Rebhan M et al (2008) Lineage-specific polycomb targets and de novo DNA methylation define restriction and potential of neuronal progenitors. Mol Cell 30:755–766
Bartke T, Vermeulen M, Xhemalce B et al (2010) Nucleosome-interacting proteins regulated by DNA and histone methylation. Cell 143:470–484
Baubec T, Colombo DF, Wirbelauer C et al (2015) Genomic profiling of DNA methyltransferases reveals a role for DNMT3B in genic methylation. Nature. doi:10.1038/nature14176
Ringrose L, Paro R (2004) Epigenetic regulation of cellular memory by the Polycomb and Trithorax group proteins. Annu Rev Genet 38:413–443
Francis NJ, Saurin AJ, Shao Z, Kingston RE (2001) Reconstitution of a functional core polycomb repressive complex. Mol Cell 8:545–556
Levine SS, Weiss A, Erdjument-Bromage H et al (2002) The core of the polycomb repressive complex is compositionally and functionally conserved in flies and humans. Mol Cell Biol 22:6070–6078
Wang H, Wang L, Erdjument-Bromage H et al (2004) Role of histone H2A ubiquitination in Polycomb silencing. Nature 431:873–878
de Napoles M, Mermoud JE, Wakao R et al (2004) Polycomb group proteins Ring1A/B link ubiquitylation of histone H2A to heritable gene silencing and X inactivation. Dev Cell 7:663–676
Gao Z, Zhang J, Bonasio R et al (2012) PCGF homologs, CBX proteins, and RYBP define functionally distinct PRC1 family complexes. Mol Cell 45:344–356
Cao R, Wang L, Wang H et al (2002) Role of histone H3 lysine 27 methylation in Polycomb-group silencing. Science 298:1039–1043
Min J, Zhang Y, Xu R-M (2003) Structural basis for specific binding of Polycomb chromodomain to histone H3 methylated at Lys 27. Genes Dev 17:1823–1828
Wang L, Brown JL, Cao R et al (2004) Hierarchical recruitment of polycomb group silencing complexes. Mol Cell 14:637–646
Blackledge NP, Farcas AM, Kondo T et al (2014) Variant PRC1 complex-dependent H2A ubiquitylation drives PRC2 recruitment and polycomb domain formation. Cell 157:1445–1459
Cooper S, Dienstbier M, Hassan R et al (2014) Targeting polycomb to pericentric heterochromatin in embryonic stem cells reveals a role for H2AK119u1 in PRC2 recruitment. Cell Rep 7:1456–1470
Kalb R, Latwiel S, Baymaz HI et al (2014) Histone H2A monoubiquitination promotes histone H3 methylation in Polycomb repression. Nat Struct Mol Biol 21:569–571
Ingham PW (1983) Differential expression of bithorax complex genes in the absence of the extra sex combs and trithorax genes. Nature 306:591–593
Klymenko T, Muller J (2004) The histone methyltransferases Trithorax and Ash1 prevent transcriptional silencing by Polycomb group proteins. EMBO Rep 5:373–377
Hanson RD, Hess JL, Yu BD et al (1999) Mammalian Trithorax and polycomb-group homologues are antagonistic regulators of homeotic development. Proc Natl Acad Sci USA 96:14372–14377
Papp B, Muller J (2006) Histone trimethylation and the maintenance of transcriptional ON and OFF states by trxG and PcG proteins. Genes Dev 20:2041–2054
Srinivasan S, Dorighi KM, Tamkun JW (2008) Drosophila Kismet regulates histone H3 lysine 27 methylation and early elongation by RNA polymerase II. PLoS Genet 4:e1000217
Yuan W, Xu M, Huang C et al (2011) H3K36 methylation antagonizes PRC2-mediated H3K27 methylation. J Biol Chem 286:7983–7989
Schmitges FW, Prusty AB, Faty M et al (2011) Histone methylation by PRC2 is inhibited by active chromatin marks. Mol Cell 42:330–341
Bernstein BE, Mikkelsen TS, Xie X et al (2006) A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell 125:315–326
Young NL, DiMaggio PA, Plazas-Mayorca MD et al (2009) High throughput characterization of combinatorial histone codes. Mol Cell Proteomics 8:2266–2284
Barski A, Cuddapah S, Cui K et al (2007) High-resolution profiling of histone methylations in the human genome. Cell 129:823–837
Schwartz YB, Pirrotta V (2008) Polycomb complexes and epigenetic states. Curr Opin Cell Biol 20:266–273
Yuan G, Ma B, Yuan W et al (2013) Histone H2A ubiquitination inhibits the enzymatic activity of H3 lysine 36 methyltransferases. J Biol Chem 288:30832–30842
Yuan W, Wu T, Fu H et al (2012) Dense chromatin activates Polycomb repressive complex 2 to regulate H3 lysine 27 methylation. Science 337:971–975
Lee C-H, Wu J, Li B (2013) Chromatin remodelers fine-tune H3K36me-directed deacetylation of neighbor nucleosomes by Rpd3S. Mol Cell 52:255–263
Hwang WL, Deindl S, Harada BT, Zhuang X (2014) Histone H4 tail mediates allosteric regulation of nucleosome remodelling by linker DNA. Nature 512:213–217
Fischle W, Wang Y, Allis CD (2003) Binary switches and modification cassettes in histone biology and beyond. Nature 425:475–479
Fischle W, Tseng BS, Dormann HL et al (2005) Regulation of HP1-chromatin binding by histone H3 methylation and phosphorylation. Nature 438:1116–1122
Varier RA, Outchkourov NS, de Graaf P et al (2010) A phospho/methyl switch at histone H3 regulates TFIID association with mitotic chromosomes. EMBO J 29:3967–3978
Zippo A, Serafini R, Rocchigiani M et al (2009) Histone crosstalk between H3S10ph and H4K16ac generates a histone code that mediates transcription elongation. Cell 138:1122–1136
Migliori V, Phalke S, Bezzi M, Guccione E (2010) Arginine/lysine-methyl/methyl switches: biochemical role of histone arginine methylation in transcriptional regulation. Epigenomics 2:119–137
Hyllus D, Stein C, Schnabel K et al (2007) PRMT6-mediated methylation of R2 in histone H3 antagonizes H3 K4 trimethylation. Genes Dev 21:3369–3380
Pal S, Vishwanath SN, Erdjument-Bromage H et al (2004) Human SWI/SNF-associated PRMT5 methylates histone H3 arginine 8 and negatively regulates expression of ST7 and NM23 tumor suppressor genes. Mol Cell Biol 24:9630–9645
Stucki M, Clapperton JA, Mohammad D et al (2005) MDC1 directly binds phosphorylated histone H2AX to regulate cellular responses to DNA double-strand breaks. Cell 123:1213–1226
Margueron R, Justin N, Ohno K et al (2009) Role of the polycomb protein EED in the propagation of repressive histone marks. Nature 461:762–767
Liu N, Zhang Z, Wu H et al (2015) Recognition of H3K9 methylation by GLP is required for efficient establishment of H3K9 methylation, rapid target gene repression, and mouse viability. Genes Dev 29:379–393