Bibliography
- Turner BM : Decoding the nucleosome.Cell75(1) , 5–8 (1993).
- Strahl BD , AllisCD: The language of covalent histone modifications.Nature403(6765) , 41–45 (2000).
- Turner BM : Reading signals on the nucleosome with a new nomenclature for modified histones.Nat. Struct. Mol. Biol.12(2) , 110–112 (2005).
- Berger SL , KouzaridesT, ShiekhattarR, ShilatifardA: An operational definition of epigenetics.Genes Dev.23(7) , 781–783 (2009).
- Bannister AJ , KouzaridesT: Regulation of chromatin by histone modifications.Cell Res.21(3) , 381–395 (2011).
- Portela A , EstellerM: Epigenetic modifications and human disease.Nat. Biotechnol.28(10) , 1057–1068 (2010).
- Young NL , DimaggioPA, GarciaBA: The significance, development and progress of high-throughput combinatorial histone code analysis.Cell. Mol. Life Sci.67(23) , 3983–4000 (2010).
- Fischle W : Talk is cheap – crosstalk in establishment, maintenance, and readout of chromatin modifications.Genes Dev.22(24) , 3375–3382 (2008).
- Winter S , FischleW: Epigenetic markers and their crosstalk.Essays Biochem.48(1) , 45–61 (2010).
- Phelan ML , SchnitzlerGR, KingstonRE: Octamer transfer and creation of stably remodeled nucleosomes by human SWI-SNF and its isolated ATPases.Mol. Cell. Biol.20(17) , 6380–6389 (2000).
- Shen W , XuC, HuangWet al.: Solution structure of human Brg1 bromodomain and its specific binding to acetylated histone tails.Biochemistry46(8) , 2100–2110 (2007).
- Collins RE , NorthropJP, HortonJRet al.: The ankyrin repeats of G9a and GLP histone methyltransferases are mono- and dimethyllysine binding modules.Nat. Struct. Mol. Biol.15(3) , 245–250 (2008).
- Collins R , ChengX: A case study in crosstalk: the histone lysine methyltransferases G9a and GLP.Nucleic Acids Res.38(11) , 3503–3511 (2010).
- Tachibana M , UedaJ, FukudaMet al.: Histone methyltransferases G9a and GLP form heteromeric complexes and are both crucial for methylation of euchromatin at H3-K9.Genes Dev.19(7) , 815–826 (2005).
- Wu H , ChenX, XiongJet al.: Histone methyltransferase G9a contributes to H3K27 methylation in vivo.Cell Res.21(2) , 365–367 (2010).
- Heintzman ND , StuartRK, HonGet al.: Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome.Nat. Genet.39(3) , 311–318 (2007).
- Creyghton MP , ChengAW, WelsteadGGet al.: Histone H3K27ac separates active from poised enhancers and predicts developmental state.Proc. Natl Acad. Sci. USA107(50) , 21931–21936 (2010).
- Hon G , RenB, WangW: ChromaSig: a probabilistic approach to finding common chromatin signatures in the human genome.PLoS Comput. Biol.4(10) , e1000201 (2008).
- Hon G , WangW, RenB: Discovery and annotation of functional chromatin signatures in the human genome.PLoS Comput. Biol.5(11) , e1000566 (2009).
- Xu X , HoangS, MayoMW, BekiranovS: Application of machine learning methods to histone methylation ChIP-Seq data reveals H4R3me2 globally represses gene expression.BMC Bioinformatics11 , 396 (2010).
- Bernstein BE , MikkelsenTS, XieXet al.: A bivalent chromatin structure marks key developmental genes in embryonic stem cells.Cell125(2) , 315–326 (2006).
- Mikkelsen TS , KuM, JaffeDBet al.: Genome-wide maps of chromatin state in pluripotent and lineage-committed cells.Nature448(7153) , 553–560 (2007).
- Zhao Q , RankG, TanYTet al.: PRMT5-mediated methylation of histone H4R3 recruits DNMT3A, coupling histone and DNA methylation in gene silencing.Nat. Struct. Mol. Biol.16(3) , 304–311 (2009).
- Barski A , CuddapahS, CuiKet al.: High-resolution profiling of histone methylations in the human genome.Cell129(4) , 823–837 (2007).
- Egelhofer TA , MinodaA, KlugmanSet al.: An assessment of histone-modification antibody quality.Nat. Struct. Mol. Biol.18(1) , 91–93 (2011).
- Fuchs SM , KrajewskiK, BakerRW, MillerVL, StrahlBD: Influence of combinatorial histone modifications on antibody and effector protein recognition.Curr. Biol.21(1) , 53–58 (2011).
- Eberl HC , MannM, VermeulenM: Quantitative proteomics for epigenetics.Chembiochem12(2) , 224–234 (2011).
- Young NL , DimaggioPA, Plazas-MayorcaMD, BalibanRC, FloudasCA, GarciaBA: High throughput characterization of combinatorial histone codes.Mol. Cell. Proteomics8(10) , 2266–2284 (2009).
- Pesavento JJ , BullockCR, LeducRD, MizzenCA, KelleherNL: Combinatorial modification of human histone H4 quantitated by two-dimensional liquid chromatography coupled with top down mass spectrometry.J. Biol. Chem.283(22) , 14927–14937 (2008).
- Phanstiel D , BrumbaughJ, BerggrenWTet al.: Mass spectrometry identifies and quantifies 74 unique histone H4 isoforms in differentiating human embryonic stem cells.Proc. Natl Acad. Sci. USA105(11) , 4093–4098 (2008).
- Scharf AN , MeierK, SeitzV, KremmerE, BrehmA, ImhofA: Monomethylation of lysine 20 on histone H4 facilitates chromatin maturation.Mol. Cell. Biol.29(1) , 57–67 (2009).
- Plazas-Mayorca MD , BloomJS, ZeisslerUet al.: Quantitative proteomics reveals direct and indirect alterations in the histone code following methyltransferase knockdown.Mol. Biosyst.6(9) , 1719–1729 (2010).
- Chaturvedi CP , HoseyAM, PaliiCet al.: Dual role for the methyltransferase G9a in the maintenance of β-globin gene transcription in adult erythroid cells.Proc. Natl Acad. Sci. USA106(43) , 18303–18308 (2009).
- Bannister AJ , SchneiderR, MyersFA, ThorneAW, Crane-RobinsonC, KouzaridesT: Spatial distribution of di- and tri-methyl lysine 36 of histone H3 at active genes.J. Biol. Chem.280(18) , 17732–17736 (2005).
- Carrozza MJ , LiB, FlorensLet al.: Histone H3 methylation by Set2 directs deacetylation of coding regions by Rpd3S to suppress spurious intragenic transcription.Cell123(4) , 581–592 (2005).
- Lim JH , WestKL, RubinsteinY, BergelM, PostnikovYV, BustinM: Chromosomal protein HMGN1 enhances the acetylation of lysine 14 in histone H3.EMBO J.24(17) , 3038–3048 (2005).
- Wu SF , ZhangH, CairnsBR: Genes for embryo development are packaged in blocks of multivalent chromatin in zebrafish sperm.Genome Res.21(4) , 578–589 (2011).
- Pasini D , MalatestaM, JungHRet al.: Characterization of an antagonistic switch between histone H3 lysine 27 methylation and acetylation in the transcriptional regulation of Polycomb group target genes.Nucleic Acids Res.38(15) , 4958–4969 (2010).
- Dover J , SchneiderJ, Tawiah-BoatengMAet al.: Methylation of histone H3 by COMPASS requires ubiquitination of histone H2B by Rad6.J. Biol. Chem.277(32) , 28368–28371 (2002).
- Lee JS , ShuklaA, SchneiderJet al.: Histone crosstalk between H2B monoubiquitination and H3 methylation mediated by COMPASS.Cell131(6) , 1084–1096 (2007).
- Ooi L , WoodIC: Chromatin crosstalk in development and disease: lessons from REST.Nat. Rev. Genet.8(7) , 544–554 (2007).
- Ooi L , BelyaevND, MiyakeK, WoodIC, BuckleyNJ: BRG1 chromatin remodeling activity is required for efficient chromatin binding by repressor element 1-silencing transcription factor (REST) and facilitates REST-mediated repression.J. Biol. Chem.281(51) , 38974–38980 (2006).
- Bingham AJ , OoiL, KozeraL, WhiteE, WoodIC: The repressor element 1-silencing transcription factor regulates heart-specific gene expression using multiple chromatin-modifying complexes.Mol. Cell. Biol.27(11) , 4082–4092 (2007).
- Lee MG , WynderC, CoochN, ShiekhattarR: An essential role for CoREST in nucleosomal histone 3 lysine 4 demethylation.Nature437(7057) , 432–435 (2005).
- Shi YJ , MatsonC, LanF, IwaseS, BabaT, ShiY: Regulation of LSD1 histone demethylase activity by its associated factors.Mol. Cell19(6) , 857–864 (2005).
- Binda O , LeroyG, BuaDJ, GarciaBA, GozaniO, RichardS: Trimethylation of histone H3 lysine 4 impairs methylation of histone H3 lysine 9: regulation of lysine methyltransferases by physical interaction with their substrates.Epigenetics5(8) , 767–775 (2010).
- Fuks F : DNA methylation and histone modifications: teaming up to silence genes.Curr. Opin. Genet. Dev.15(5) , 490–495 (2005).
- Kazantseva A , SeppM, KazantsevaJet al.: N-terminally truncated BAF57 isoforms contribute to the diversity of SWI/SNF complexes in neurons.J. Neurochem.109(3) , 807–818 (2009).
- Schaniel C , AngYS, RatnakumarKet al.: Smarcc1/Baf155 couples self-renewal gene repression with changes in chromatin structure in mouse embryonic stem cells.Stem Cells27(12) , 2979–2991 (2009).
- Wang Z , ZangC, CuiKet al.: Genome-wide mapping of HATs and HDACs reveals distinct functions in active and inactive genes.Cell138(5) , 1019–1031 (2009).
- Shi X , HongT, WalterKLet al.: ING2 PHD domain links histone H3 lysine 4 methylation to active gene repression.Nature442(7098) , 96–99 (2006).
- Hung T , BindaO, ChampagneKSet al.: ING4 mediates crosstalk between histone H3 K4 trimethylation and H3 acetylation to attenuate cellular transformation.Mol. Cell33(2) , 248–256 (2009).
- Guccione E , BassiC, CasadioFet al.: Methylation of histone H3R2 by PRMT6 and H3K4 by an MLL complex are mutually exclusive.Nature449(7164) , 933–937 (2007).
- Kirmizis A , Santos-RosaH, PenkettCJet al.: Arginine methylation at histone H3R2 controls deposition of H3K4 trimethylation.Nature449(7164) , 928–932 (2007).
- Rathert P , DhayalanA, MurakamiMet al.: Protein lysine methyltransferase G9a acts on non-histone targets.Nat. Chem. Biol.4(6) , 344–346 (2008).
- Fischle W , TsengBS, DormannHLet al.: Regulation of HP1-chromatin binding by histone H3 methylation and phosphorylation.Nature438(7071) , 1116–1122 (2005).
- Hirota T , LippJJ, TohBH, PetersJM: Histone H3 serine 10 phosphorylation by Aurora B causes HP1 dissociation from heterochromatin.Nature438(7071) , 1176–1180 (2005).
- Yuan W , XuM, HuangC, LiuN, ChenS, ZhuB: H3K36 methylation antagonizes PRC2 mediated H3K27 methylation.J. Biol. Chem.286(10) , 7983–7989 (2011).