3,157
Views
50
CrossRef citations to date
0
Altmetric
Review

On your histone mark, SET, methylate!

Pages 457-463 | Received 05 Mar 2013, Accepted 26 Mar 2013, Published online: 27 Apr 2013

References

  • Jenuwein T, Allis CD. Translating the histone code. Science 2001; 293:1074 - 80; http://dx.doi.org/10.1126/science.1063127; PMID: 11498575
  • Barski A, Cuddapah S, Cui K, Roh T-Y, Schones DE, Wang Z, et al. High-resolution profiling of histone methylations in the human genome. Cell 2007; 129:823 - 37; http://dx.doi.org/10.1016/j.cell.2007.05.009; PMID: 17512414
  • Shi X, Hong T, Walter KL, Ewalt M, Michishita E, Hung T, et al. ING2 PHD domain links histone H3 lysine 4 methylation to active gene repression. Nature 2006; 442:96 - 9; PMID: 16728974
  • Bua DJ, Binda O. The return of the INGs, histone mark sensors and phospholipid signaling effectors. Curr Drug Targets 2009; 10:418 - 31; http://dx.doi.org/10.2174/138945009788185112; PMID: 19442114
  • Hung T, Binda O, Champagne KS, Kuo AJ, Johnson K, Chang HY, et al. ING4 mediates crosstalk between histone H3 K4 trimethylation and H3 acetylation to attenuate cellular transformation. Mol Cell 2009; 33:248 - 56; http://dx.doi.org/10.1016/j.molcel.2008.12.016; PMID: 19187765
  • Sims RJ 3rd, Reinberg D. Is there a code embedded in proteins that is based on post-translational modifications?. Nat Rev Mol Cell Biol 2008; 9:815 - 20; http://dx.doi.org/10.1038/nrm2502; PMID: 18784729
  • Lee J-S, Smith E, Shilatifard A. The language of histone crosstalk. Cell 2010; 142:682 - 5; http://dx.doi.org/10.1016/j.cell.2010.08.011; PMID: 20813257
  • Henikoff S, Shilatifard A. Histone modification: cause or cog?. Trends Genet 2011; 27:389 - 96; http://dx.doi.org/10.1016/j.tig.2011.06.006; PMID: 21764166
  • Albert M, Helin K. Histone methyltransferases in cancer. Semin Cell Dev Biol 2010; 21:209 - 20; http://dx.doi.org/10.1016/j.semcdb.2009.10.007; PMID: 19892027
  • Schneider R, Bannister AJ, Kouzarides T. Unsafe SETs: histone lysine methyltransferases and cancer. Trends Biochem Sci 2002; 27:396 - 402; http://dx.doi.org/10.1016/S0968-0004(02)02141-2; PMID: 12151224
  • Morishita M, di Luccio E. Cancers and the NSD family of histone lysine methyltransferases. Biochim Biophys Acta 2011; 1816:158 - 63; PMID: 21664949
  • Ryu H, Lee J, Hagerty SW, Soh BY, McAlpin SE, Cormier KA, et al. ESET/SETDB1 gene expression and histone H3 (K9) trimethylation in Huntington’s disease. Proc Natl Acad Sci U S A 2006; 103:19176 - 81; http://dx.doi.org/10.1073/pnas.0606373103; PMID: 17142323
  • Feng Q, Wang H, Ng HH, Erdjument-Bromage H, Tempst P, Struhl K, et al. Methylation of H3-lysine 79 is mediated by a new family of HMTases without a SET domain. Curr Biol 2002; 12:1052 - 8; http://dx.doi.org/10.1016/S0960-9822(02)00901-6; PMID: 12123582
  • Min J, Feng Q, Li Z, Zhang Y, Xu R-M. Structure of the catalytic domain of human DOT1L, a non-SET domain nucleosomal histone methyltransferase. Cell 2003; 112:711 - 23; http://dx.doi.org/10.1016/S0092-8674(03)00114-4; PMID: 12628190
  • Patel A, Vought VE, Dharmarajan V, Cosgrove MS. A novel non-SET domain multi-subunit methyltransferase required for sequential nucleosomal histone H3 methylation by the mixed lineage leukemia protein-1 (MLL1) core complex. J Biol Chem 2011; 286:3359 - 69; http://dx.doi.org/10.1074/jbc.M110.174524; PMID: 21106533
  • Petrossian TC, Clarke SG. Uncovering the human methyltransferasome. Mol Cell Proteomics 2011; 10:M110.000976; http://dx.doi.org/10.1074/mcp.M110.000976; PMID: 20930037
  • Cloutier P, Lavallée-Adam M, Faubert D, Blanchette M, Coulombe B. A newly uncovered group of distantly related lysine methyltransferases preferentially interact with molecular chaperones to regulate their activity. PLoS Genet 2013; 9:e1003210; http://dx.doi.org/10.1371/journal.pgen.1003210; PMID: 23349634
  • Musselman CA, Lalonde M-È, Côté J, Kutateladze TG. Perceiving the epigenetic landscape through histone readers. Nat Struct Mol Biol 2012; 19:1218 - 27; http://dx.doi.org/10.1038/nsmb.2436; PMID: 23211769
  • Baker LA, Allis CD, Wang GG. PHD fingers in human diseases: disorders arising from misinterpreting epigenetic marks. Mutat Res 2008; 647:3 - 12; http://dx.doi.org/10.1016/j.mrfmmm.2008.07.004; PMID: 18682256
  • Musselman CA, Kutateladze TG. PHD fingers: epigenetic effectors and potential drug targets. Mol Interv 2009; 9:314 - 23; http://dx.doi.org/10.1124/mi.9.6.7; PMID: 20048137
  • Bonasio R, Lecona E, Reinberg D. MBT domain proteins in development and disease. Semin Cell Dev Biol 2010; 21:221 - 30; http://dx.doi.org/10.1016/j.semcdb.2009.09.010; PMID: 19778625
  • Wang H, Cao R, Xia L, Erdjument-Bromage H, Borchers C, Tempst P, et al. Purification and functional characterization of a histone H3-lysine 4-specific methyltransferase. Mol Cell 2001; 8:1207 - 17; http://dx.doi.org/10.1016/S1097-2765(01)00405-1; PMID: 11779497
  • Heintzman ND, Stuart RK, Hon G, Fu Y, Ching CW, Hawkins RD, et al. Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat Genet 2007; 39:311 - 8; http://dx.doi.org/10.1038/ng1966; PMID: 17277777
  • Guccione E, Bassi C, Casadio F, Martinato F, Cesaroni M, Schuchlautz H, et al. Methylation of histone H3R2 by PRMT6 and H3K4 by an MLL complex are mutually exclusive. Nature 2007; 449:933 - 7; http://dx.doi.org/10.1038/nature06166; PMID: 17898714
  • Kirmizis A, Santos-Rosa H, Penkett CJ, Singer MA, Vermeulen M, Mann M, et al. Arginine methylation at histone H3R2 controls deposition of H3K4 trimethylation. Nature 2007; 449:928 - 32; http://dx.doi.org/10.1038/nature06160; PMID: 17898715
  • Yuan C-C, Matthews AGW, Jin Y, Chen CF, Chapman BA, Ohsumi TK, et al. Histone H3R2 symmetric dimethylation and histone H3K4 trimethylation are tightly correlated in eukaryotic genomes. Cell reports 2012; 1:83 - 90; http://dx.doi.org/10.1016/j.celrep.2011.12.008; PMID: 22720264
  • Migliori V, Müller J, Phalke S, Low D, Bezzi M, Mok WC, et al. Symmetric dimethylation of H3R2 is a newly identified histone mark that supports euchromatin maintenance. Nat Struct Mol Biol 2012; 19:136 - 44; http://dx.doi.org/10.1038/nsmb.2209; PMID: 22231400
  • Eswaran J, Patnaik D, Filippakopoulos P, Wang F, Stein RL, Murray JW, et al. Structure and functional characterization of the atypical human kinase haspin. Proc Natl Acad Sci U S A 2009; 106:20198 - 203; http://dx.doi.org/10.1073/pnas.0901989106; PMID: 19918057
  • Southall SM, Wong P-S, Odho Z, Roe SM, Wilson JR. Structural basis for the requirement of additional factors for MLL1 SET domain activity and recognition of epigenetic marks. Mol Cell 2009; 33:181 - 91; http://dx.doi.org/10.1016/j.molcel.2008.12.029; PMID: 19187761
  • Chuikov S, Kurash JK, Wilson JR, Xiao B, Justin N, Ivanov GS, et al. Regulation of p53 activity through lysine methylation. Nature 2004; 432:353 - 60; http://dx.doi.org/10.1038/nature03117; PMID: 15525938
  • Munro S, Khaire N, Inche A, Carr S, La Thangue NB. Lysine methylation regulates the pRb tumour suppressor protein. Oncogene 2010; 29:2357 - 67; http://dx.doi.org/10.1038/onc.2009.511; PMID: 20140018
  • Subramanian K, Jia D, Kapoor-Vazirani P, Powell DR, Collins RE, Sharma D, et al. Regulation of estrogen receptor alpha by the SET7 lysine methyltransferase. Mol Cell 2008; 30:336 - 47; http://dx.doi.org/10.1016/j.molcel.2008.03.022; PMID: 18471979
  • Gaughan L, Stockley J, Wang N, McCracken SR, Treumann A, Armstrong K, et al. Regulation of the androgen receptor by SET9-mediated methylation. Nucleic Acids Res 2010; 39;:4 1266 - 79; http://dx.doi.org/10.1093/nar/gkq861; PMID: 20959290
  • Estève P-O, Chin HG, Benner J, Feehery GR, Samaranayake M, Horwitz GA, et al. Regulation of DNMT1 stability through SET7-mediated lysine methylation in mammalian cells. Proc Natl Acad Sci U S A 2009; 106:5076 - 81; http://dx.doi.org/10.1073/pnas.0810362106; PMID: 19282482
  • Liu X, Wang D, Zhao Y, Tu B, Zheng Z, Wang L, et al. Methyltransferase Set7/9 regulates p53 activity by interacting with Sirtuin 1 (SIRT1). Proc Natl Acad Sci U S A 2011; 108:1925 - 30; http://dx.doi.org/10.1073/pnas.1019619108; PMID: 21245319
  • Xiao B, Jing C, Wilson JR, Walker PA, Vasisht N, Kelly G, et al. Structure and catalytic mechanism of the human histone methyltransferase SET7/9. Nature 2003; 421:652 - 6; http://dx.doi.org/10.1038/nature01378; PMID: 12540855
  • Gregory GD, Vakoc CR, Rozovskaia T, Zheng X, Patel S, Nakamura T, et al. Mammalian ASH1L is a histone methyltransferase that occupies the transcribed region of active genes. Mol Cell Biol 2007; 27:8466 - 79; http://dx.doi.org/10.1128/MCB.00993-07; PMID: 17923682
  • Vermeulen M, Mulder KW, Denissov S, Pijnappel WWMP, van Schaik FMA, Varier RA, et al. Selective anchoring of TFIID to nucleosomes by trimethylation of histone H3 lysine 4. Cell 2007; 131:58 - 69; http://dx.doi.org/10.1016/j.cell.2007.08.016; PMID: 17884155
  • Varier RA, Outchkourov NS, de Graaf P, van Schaik FMA, Ensing HJL, Wang F, et al. A phospho/methyl switch at histone H3 regulates TFIID association with mitotic chromosomes. EMBO J 2010; 29:3967 - 78; http://dx.doi.org/10.1038/emboj.2010.261; PMID: 20953165
  • Dai J, Sultan S, Taylor SS, Higgins JMG. The kinase haspin is required for mitotic histone H3 Thr 3 phosphorylation and normal metaphase chromosome alignment. Genes Dev 2005; 19:472 - 88; http://dx.doi.org/10.1101/gad.1267105; PMID: 15681610
  • Huertas D, Soler M, Moreto J, Villanueva A, Martinez A, Vidal A, et al. Antitumor activity of a small-molecule inhibitor of the histone kinase Haspin. Oncogene 2012; 31:1408 - 18; http://dx.doi.org/10.1038/onc.2011.335; PMID: 21804608
  • Yang L, Xia L, Wu DY, Wang H, Chansky HA, Schubach WH, et al. Molecular cloning of ESET, a novel histone H3-specific methyltransferase that interacts with ERG transcription factor. Oncogene 2002; 21:148 - 52; http://dx.doi.org/10.1038/sj.onc.1204998; PMID: 11791185
  • Schultz DC, Ayyanathan K, Negorev D, Maul GG, Rauscher FJ 3rd. SETDB1: a novel KAP-1-associated histone H3, lysine 9-specific methyltransferase that contributes to HP1-mediated silencing of euchromatic genes by KRAB zinc-finger proteins. Genes Dev 2002; 16:919 - 32; http://dx.doi.org/10.1101/gad.973302; PMID: 11959841
  • Binda O, LeRoy G, Bua DJ, Garcia BA, Gozani O, Richard S. Trimethylation of histone H3 lysine 4 impairs methylation of histone H3 lysine 9: regulation of lysine methyltransferases by physical interaction with their substrates. Epigenetics 2010; 5:767 - 75; http://dx.doi.org/10.4161/epi.5.8.13278; PMID: 21124070
  • Wang H, An W, Cao R, Xia L, Erdjument-Bromage H, Chatton B, et al. mAM facilitates conversion by ESET of dimethyl to trimethyl lysine 9 of histone H3 to cause transcriptional repression. Mol Cell 2003; 12:475 - 87; http://dx.doi.org/10.1016/j.molcel.2003.08.007; PMID: 14536086
  • Rea S, Eisenhaber F, O’Carroll D, Strahl BD, Sun Z-W, Schmid M, et al. Regulation of chromatin structure by site-specific histone H3 methyltransferases. Nature 2000; 406:593 - 9; http://dx.doi.org/10.1038/35020506; PMID: 10949293
  • O’Carroll D, Scherthan H, Peters AH, Opravil S, Haynes AR, Laible G, et al. Isolation and characterization of Suv39h2, a second histone H3 methyltransferase gene that displays testis-specific expression. Mol Cell Biol 2000; 20:9423 - 33; http://dx.doi.org/10.1128/MCB.20.24.9423-9433.2000; PMID: 11094092
  • Tachibana M, Sugimoto K, Fukushima T, Shinkai Y. Set domain-containing protein, G9a, is a novel lysine-preferring mammalian histone methyltransferase with hyperactivity and specific selectivity to lysines 9 and 27 of histone H3. J Biol Chem 2001; 276:25309 - 17; http://dx.doi.org/10.1074/jbc.M101914200; PMID: 11316813
  • Kim K-C, Geng L, Huang S. Inactivation of a histone methyltransferase by mutations in human cancers. Cancer Res 2003; 63:7619 - 23; PMID: 14633678
  • Fritsch L, Robin P, Mathieu JRR, Souidi M, Hinaux H, Rougeulle C, et al. A subset of the histone H3 lysine 9 methyltransferases Suv39h1, G9a, GLP, and SETDB1 participate in a multimeric complex. Mol Cell 2010; 37:46 - 56; http://dx.doi.org/10.1016/j.molcel.2009.12.017; PMID: 20129054
  • Wu M, Wang PF, Lee JS, Martin-Brown S, Florens L, Washburn M, et al. Molecular regulation of H3K4 trimethylation by Wdr82, a component of human Set1/COMPASS. Mol Cell Biol 2008; 28:7337 - 44; http://dx.doi.org/10.1128/MCB.00976-08; PMID: 18838538
  • Nishioka K, Chuikov S, Sarma K, Erdjument-Bromage H, Allis CD, Tempst P, et al. Set9, a novel histone H3 methyltransferase that facilitates transcription by precluding histone tail modifications required for heterochromatin formation. Genes Dev 2002; 16:479 - 89; http://dx.doi.org/10.1101/gad.967202; PMID: 11850410
  • Wu H, Min J, Lunin VV, Antoshenko T, Dombrovski L, Zeng H, et al. Structural biology of human H3K9 methyltransferases. PLoS One 2010; 5:e8570; http://dx.doi.org/10.1371/journal.pone.0008570; PMID: 20084102
  • Pal S, Vishwanath SN, Erdjument-Bromage H, Tempst P, Sif S. Human SWI/SNF-associated PRMT5 methylates histone H3 arginine 8 and negatively regulates expression of ST7 and NM23 tumor suppressor genes. Mol Cell Biol 2004; 24:9630 - 45; http://dx.doi.org/10.1128/MCB.24.21.9630-9645.2004; PMID: 15485929
  • Duan Q, Chen H, Costa M, Dai W. Phosphorylation of H3S10 blocks the access of H3K9 by specific antibodies and histone methyltransferase. Implication in regulating chromatin dynamics and epigenetic inheritance during mitosis. J Biol Chem 2008; 283:33585 - 90; http://dx.doi.org/10.1074/jbc.M803312200; PMID: 18835819
  • Fischle W, Tseng BS, Dormann HL, Ueberheide BM, Garcia BA, Shabanowitz J, et al. Regulation of HP1-chromatin binding by histone H3 methylation and phosphorylation. Nature 2005; 438:1116 - 22; http://dx.doi.org/10.1038/nature04219; PMID: 16222246
  • Hirota T, Lipp JJ, Toh B-H, Peters J-M. Histone H3 serine 10 phosphorylation by Aurora B causes HP1 dissociation from heterochromatin. Nature 2005; 438:1176 - 80; http://dx.doi.org/10.1038/nature04254; PMID: 16222244
  • Lachner M, O’Carroll D, Rea S, Mechtler K, Jenuwein T. Methylation of histone H3 lysine 9 creates a binding site for HP1 proteins. Nature 2001; 410:116 - 20; http://dx.doi.org/10.1038/35065132; PMID: 11242053
  • Shen X, Liu Y, Hsu Y-J, Fujiwara Y, Kim J, Mao X, et al. EZH1 mediates methylation on histone H3 lysine 27 and complements EZH2 in maintaining stem cell identity and executing pluripotency. Mol Cell 2008; 32:491 - 502; http://dx.doi.org/10.1016/j.molcel.2008.10.016; PMID: 19026780
  • Cao R, Wang L, Wang H, Xia L, Erdjument-Bromage H, Tempst P, et al. Role of histone H3 lysine 27 methylation in Polycomb-group silencing. Science 2002; 298:1039 - 43; http://dx.doi.org/10.1126/science.1076997; PMID: 12351676
  • Schurter BT, Koh SS, Chen D, Bunick GJ, Harp JM, Hanson BL, et al. Methylation of histone H3 by coactivator-associated arginine methyltransferase 1. Biochemistry 2001; 40:5747 - 56; http://dx.doi.org/10.1021/bi002631b; PMID: 11341840
  • Zhong S, Jansen C, She QB, Goto H, Inagaki M, Bode AM, et al. Ultraviolet B-induced phosphorylation of histone H3 at serine 28 is mediated by MSK1. J Biol Chem 2001; 276:33213 - 9; http://dx.doi.org/10.1074/jbc.M103973200; PMID: 11441012
  • Bonenfant D, Towbin H, Coulot M, Schindler P, Mueller DR, van Oostrum J. Analysis of dynamic changes in post-translational modifications of human histones during cell cycle by mass spectrometry. Mol Cell Proteomics 2007; 6:1917 - 32; http://dx.doi.org/10.1074/mcp.M700070-MCP200; PMID: 17644761
  • Vermeulen M, Eberl HC, Matarese F, Marks H, Denissov S, Butter F, et al. Quantitative interaction proteomics and genome-wide profiling of epigenetic histone marks and their readers. Cell 2010; 142:967 - 80; http://dx.doi.org/10.1016/j.cell.2010.08.020; PMID: 20850016
  • Sawada K, Yang Z, Horton JR, Collins RE, Zhang X, Cheng X. Structure of the conserved core of the yeast Dot1p, a nucleosomal histone H3 lysine 79 methyltransferase. J Biol Chem 2004; 279:43296 - 306; http://dx.doi.org/10.1074/jbc.M405902200; PMID: 15292170
  • Nishioka K, Rice JC, Sarma K, Erdjument-Bromage H, Werner J, Wang Y, et al. PR-Set7 is a nucleosome-specific methyltransferase that modifies lysine 20 of histone H4 and is associated with silent chromatin. Mol Cell 2002; 9:1201 - 13; http://dx.doi.org/10.1016/S1097-2765(02)00548-8; PMID: 12086618
  • Tan M, Luo H, Lee S, Jin F, Yang JS, Montellier E, et al. Identification of 67 histone marks and histone lysine crotonylation as a new type of histone modification. Cell 2011; 146:1016 - 28; http://dx.doi.org/10.1016/j.cell.2011.08.008; PMID: 21925322
  • Couture J-F, Collazo E, Brunzelle JS, Trievel RC. Structural and functional analysis of SET8, a histone H4 Lys-20 methyltransferase. Genes Dev 2005; 19:1455 - 65; http://dx.doi.org/10.1101/gad.1318405; PMID: 15933070
  • Tang J, Cho NW, Cui G, Manion EM, Shanbhag NM, Botuyan MV, et al. Acetylation limits 53BP1 association with damaged chromatin to promote homologous recombination. Nat Struct Mol Biol 2013; 20:317 - 25; http://dx.doi.org/10.1038/nsmb.2499; PMID: 23377543
  • Botuyan MV, Lee J, Ward IM, Kim J-E, Thompson JR, Chen J, et al. Structural basis for the methylation state-specific recognition of histone H4-K20 by 53BP1 and Crb2 in DNA repair. Cell 2006; 127:1361 - 73; http://dx.doi.org/10.1016/j.cell.2006.10.043; PMID: 17190600
  • Sanders SL, Portoso M, Mata J, Bähler J, Allshire RC, Kouzarides T. Methylation of histone H4 lysine 20 controls recruitment of Crb2 to sites of DNA damage. Cell 2004; 119:603 - 14; http://dx.doi.org/10.1016/j.cell.2004.11.009; PMID: 15550243
  • Binda O, Sevilla A, Leroy G, Lemischka IR, Garcia BA, Richard S. SETD6 monomethylates H2AZ on lysine 7 and is required for the maintenance of embryonic stem cell self-renewal. Epigenetics 2013; 8:177 - 83; http://dx.doi.org/10.4161/epi.23416; PMID: 23324626
  • Huang J, Perez-Burgos L, Placek BJ, Sengupta R, Richter M, Dorsey JA, et al. Repression of p53 activity by Smyd2-mediated methylation. Nature 2006; 444:629 - 32; http://dx.doi.org/10.1038/nature05287; PMID: 17108971
  • Wang L, Li L, Zhang H, Luo X, Dai J, Zhou S, et al. Structure of human SMYD2 protein reveals the basis of p53 tumor suppressor methylation. J Biol Chem 2011; 286:38725 - 37; http://dx.doi.org/10.1074/jbc.M111.262410; PMID: 21880715
  • Huang J, Dorsey J, Chuikov S, Pérez-Burgos L, Zhang X, Jenuwein T, et al. G9a and Glp methylate lysine 373 in the tumor suppressor p53. J Biol Chem 2010; 285:9636 - 41; http://dx.doi.org/10.1074/jbc.M109.062588; PMID: 20118233
  • Huang J, Sengupta R, Espejo AB, Lee MG, Dorsey JA, Richter M, et al. p53 is regulated by the lysine demethylase LSD1. Nature 2007; 449:105 - 8; http://dx.doi.org/10.1038/nature06092; PMID: 17805299
  • Shi X, Kachirskaia I, Yamaguchi H, West LE, Wen H, Wang EW, et al. Modulation of p53 function by SET8-mediated methylation at lysine 382. Mol Cell 2007; 27:636 - 46; http://dx.doi.org/10.1016/j.molcel.2007.07.012; PMID: 17707234
  • West LE, Roy S, Lachmi-Weiner K, Hayashi R, Shi X, Appella E, et al. The MBT repeats of L3MBTL1 link SET8-mediated p53 methylation at lysine 382 to target gene repression. J Biol Chem 2010; 285:37725 - 32; http://dx.doi.org/10.1074/jbc.M110.139527; PMID: 20870725
  • Kachirskaia I, Shi X, Yamaguchi H, Tanoue K, Wen H, Wang EW, et al. Role for 53BP1 Tudor domain recognition of p53 dimethylated at lysine 382 in DNA damage signaling. J Biol Chem 2008; 283:34660 - 6; http://dx.doi.org/10.1074/jbc.M806020200; PMID: 18840612
  • Estève P-O, Chang Y, Samaranayake M, Upadhyay AK, Horton JR, Feehery GR, et al. A methylation and phosphorylation switch between an adjacent lysine and serine determines human DNMT1 stability. Nat Struct Mol Biol 2011; 18:42 - 8; http://dx.doi.org/10.1038/nsmb.1939; PMID: 21151116