Akhtar W, Pindyurin AV, de Jong J, Pagie L, Ten Hoeve J, Berns A, Wessels LF, van Steensel B, van Lohuizen M (2014) Using TRIP for genome-wide position effect analysis in cultured cells. Nat Protoc 9(6):1255–1281
CAS
PubMed
Article
Google Scholar
An S, Yeo KJ, Jeon YH, Song JJ (2011) Crystal structure of the human histone methyltransferase ASH1L catalytic domain and its implications for the regulatory mechanism. J Biol Chem 286(10):8369–8374
CAS
PubMed
PubMed Central
Article
Google Scholar
Arnold P, Scholer A, Pachkov M, Balwierz PJ, Jorgensen H, Stadler MB, van Nimwegen E, Schubeler D (2013) Modeling of epigenome dynamics identifies transcription factors that mediate Polycomb targeting. Genome Res 23(1):60–73
CAS
PubMed
PubMed Central
Article
Google Scholar
Atchison L, Ghias A, Wilkinson F, Bonini N, Atchison ML (2003) Transcription factor YY1 functions as a PcG protein in vivo. EMBO J 22(6):1347–1358
CAS
PubMed
PubMed Central
Article
Google Scholar
Basu A, Dasari V, Mishra RK, Khosla S (2014) The CpG island encompassing the promoter and first exon of human DNMT3L gene is a PcG/TrX response element (PRE). PLoS One 9(4):e93561
PubMed
PubMed Central
Article
CAS
Google Scholar
Bengani H, Ganapathi M, Singh GP, Brahmachari V (2007) Mining of putative cis-acting elements for chromatin mediated regulation of Hox genes in mammals by in-silico analysis. J Exp Zool B Mol Dev Evol 308(4):384–395
PubMed
Article
CAS
Google Scholar
Bengani H, Mendiratta S, Maini J, Vasanthi D, Sultana H, Ghasemi M, Ahluwalia J, Ramachandran S, Mishra RK, Brahmachari V (2013) Identification and validation of a putative Polycomb responsive element in the human genome. PLoS One 8(6):e67217
CAS
PubMed
PubMed Central
Article
Google Scholar
Bernstein BE, Mikkelsen TS, Xie X, Kamal M, Huebert DJ, Cuff J, Fry B, Meissner A, Wernig M, Plath K, Jaenisch R, Wagschal A, Feil R, Schreiber SL, Lander ES (2006a) A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell 125(2):315–326
CAS
PubMed
Article
Google Scholar
Bernstein E, Duncan EM, Masui O, Gil J, Heard E, Allis CD (2006b) Mouse polycomb proteins bind differentially to methylated histone H3 and RNA and are enriched in facultative heterochromatin. Mol Cell Biol 26(7):2560–2569
CAS
PubMed
PubMed Central
Article
Google Scholar
Beuchle D, Struhl G, Muller J (2001) Polycomb group proteins and heritable silencing of Drosophila Hox genes. Development 128(6):993–1004
CAS
PubMed
Google Scholar
Biggin MD, Bickel S, Benson M, Pirrotta V, Tjian R (1988) Zeste encodes a sequence-specific transcription factor that activates the ultrabithorax promoter in vitro. Cell 53(5):713–722
CAS
PubMed
Article
Google Scholar
Blackledge NP, Farcas AM, Kondo T, King HW, McGouran JF, Hanssen LL, Ito S, Cooper S, Kondo K, Koseki Y, Ishikura T, Long HK, Sheahan TW, Brockdorff N, Kessler BM, Koseki H, Klose RJ (2014) Variant PRC1 complex-dependent H2A ubiquitylation drives PRC2 recruitment and polycomb domain formation. Cell 157(6):1445–1459
CAS
PubMed
PubMed Central
Article
Google Scholar
Blastyak A, Mishra RK, Karch F, Gyurkovics H (2006) Efficient and specific targeting of Polycomb group proteins requires cooperative interaction between grainyhead and pleiohomeotic. Mol Cell Biol 26(4):1434–1444
CAS
PubMed
PubMed Central
Article
Google Scholar
Boulard M, Edwards JR, Bestor TH (2015) FBXL10 protects Polycomb-bound genes from hypermethylation. Nat Genet 47(5):479–485
CAS
PubMed
Article
Google Scholar
Bowers SR, Calero-Nieto FJ, Valeaux S, Fernandez-Fuentes N, Cockerill PN (2010) Runx1 binds as a dimeric complex to overlapping Runx1 sites within a palindromic element in the human GM-CSF enhancer. Nucleic Acids Res 38(18):6124–6134
CAS
PubMed
PubMed Central
Article
Google Scholar
Bowman SK, Deaton AM, Domingues H, Wang PI, Sadreyev RI, Kingston RE, Bender W (2014) H3K27 modifications define segmental regulatory domains in the Drosophila bithorax complex. Elife 3:e02833
PubMed
PubMed Central
Article
CAS
Google Scholar
Briggs MR, Kadonaga JT, Bell SP, Tjian R (1986) Purification and biochemical characterization of the promoter-specific transcription factor, Sp1. Science 234(4772):47–52
CAS
PubMed
Article
Google Scholar
Brinkman AB, Gu H, Bartels SJ, Zhang Y, Matarese F, Simmer F, Marks H, Bock C, Gnirke A, Meissner A, Stunnenberg HG (2012) Sequential ChIP-bisulfite sequencing enables direct genome-scale investigation of chromatin and DNA methylation cross-talk. Genome Res 22(6):1128–1138
CAS
PubMed
PubMed Central
Article
Google Scholar
Brockdorff N (2013) Noncoding RNA and Polycomb recruitment. RNA 19(4):429–442
CAS
PubMed
PubMed Central
Article
Google Scholar
Brookes E, de Santiago I, Hebenstreit D, Morris KJ, Carroll T, Xie SQ, Stock JK, Heidemann M, Eick D, Nozaki N, Kimura H, Ragoussis J, Teichmann SA, Pombo A (2012) Polycomb associates genome-wide with a specific RNA polymerase II variant, and regulates metabolic genes in ESCs. Cell Stem Cell 10(2):157–170
CAS
PubMed
PubMed Central
Article
Google Scholar
Brown JL, Mucci D, Whiteley M, Dirksen ML, Kassis JA (1998) The Drosophila Polycomb group gene pleiohomeotic encodes a DNA binding protein with homology to the transcription factor YY1. Mol Cell 1(7):1057–1064
CAS
PubMed
Article
Google Scholar
Brown JL, Fritsch C, Mueller J, Kassis JA (2003) The Drosophila pho-like gene encodes a YY1-related DNA binding protein that is redundant with pleiohomeotic in homeotic gene silencing. Development 130(2):285–294
CAS
PubMed
Article
Google Scholar
Brown JL, Grau DJ, DeVido SK, Kassis JA (2005) An Sp1/KLF binding site is important for the activity of a Polycomb group response element from the Drosophila engrailed gene. Nucleic Acids Res 33(16):5181–5189
CAS
PubMed
PubMed Central
Article
Google Scholar
Cabianca DS, Casa V, Bodega B, Xynos A, Ginelli E, Tanaka Y, Gabellini D (2012) A long ncRNA links copy number variation to a polycomb/trithorax epigenetic switch in FSHD muscular dystrophy. Cell 149(4):819–831
CAS
PubMed
PubMed Central
Article
Google Scholar
Cao R, Zhang Y (2004) SUZ12 is required for both the histone methyltransferase activity and the silencing function of the EED-EZH2 complex. Mol Cell 15(1):57–67
CAS
PubMed
Article
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(5595):1039–1043
CAS
PubMed
Article
Google Scholar
Cao R, Tsukada Y, Zhang Y (2005) Role of Bmi-1 and Ring1A in H2A ubiquitylation and Hox gene silencing. Mol Cell 20(6):845–854
CAS
PubMed
Article
Google Scholar
Caputo VS, Costa JR, Makarona K, Georgiou E, Layton DM, Roberts I, Karadimitris A (2013) Mechanism of Polycomb recruitment to CpG islands revealed by inherited disease-associated mutation. Hum Mol Genet 22(16):3187–3194
CAS
PubMed
Article
Google Scholar
Cavalli G, Paro R (1998) The Drosophila Fab-7 chromosomal element conveys epigenetic inheritance during mitosis and meiosis. Cell 93(4):505–518
CAS
PubMed
Article
Google Scholar
Cerase A, Smeets D, Tang YA, Gdula M, Kraus F, Spivakov M, Moindrot B, Leleu M, Tattermusch A, Demmerle J, Nesterova TB, Green C, Otte AP, Schermelleh L, Brockdorff N (2014) Spatial separation of Xist RNA and polycomb proteins revealed by superresolution microscopy. Proc Natl Acad Sci U S A 111(6):2235–2240
CAS
PubMed
PubMed Central
Article
Google Scholar
Chan CS, Rastelli L, Pirrotta V (1994) A Polycomb response element in the Ubx gene that determines an epigenetically inherited state of repression. EMBO J 13(11):2553–2564
CAS
PubMed
PubMed Central
Google Scholar
Cheutin T, Cavalli G (2014) Polycomb silencing: from linear chromatin domains to 3D chromosome folding. Curr Opin Genet Dev 25:30–37
CAS
PubMed
Article
Google Scholar
Cifuentes-Rojas C, Hernandez AJ, Sarma K, Lee JT (2014) Regulatory interactions between RNA and polycomb repressive complex 2. Mol Cell 55(2):171–185
CAS
PubMed
PubMed Central
Article
Google Scholar
Cooper S, Dienstbier M, Hassan R, Schermelleh L, Sharif J, Blackledge NP, De Marco V, Elderkin S, Koseki H, Klose R, Heger A, Brockdorff N (2014) Targeting polycomb to pericentric heterochromatin in embryonic stem cells reveals a role for H2AK119u1 in PRC2 recruitment. Cell Rep 7(5):1456–1470
CAS
PubMed
PubMed Central
Article
Google Scholar
Creppe C, Palau A, Malinverni R, Valero V, Buschbeck M (2014) A CBX8-containing polycomb complex facilitates the transition to gene activation during ES cell differentiation. PLoS Genet 10(12):e1004851
PubMed
PubMed Central
Article
CAS
Google Scholar
Cuddapah S, Roh TY, Cui K, Jose CC, Fuller MT, Zhao K, Chen X (2012) A novel human polycomb binding site acts as a functional polycomb response element in Drosophila. PLoS One 7(5):e36365
CAS
PubMed
PubMed Central
Article
Google Scholar
Czermin B, Melfi R, McCabe D, Seitz V, Imhof A, Pirrotta V (2002) Drosophila enhancer of Zeste/ESC complexes have a histone H3 methyltransferase activity that marks chromosomal Polycomb sites. Cell 111(2):185–196
CAS
PubMed
Article
Google Scholar
Davidovich C, Zheng L, Goodrich KJ, Cech TR (2013) Promiscuous RNA binding by Polycomb repressive complex 2. Nat Struct Mol Biol 20(11):1250–1257
CAS
PubMed
PubMed Central
Article
Google Scholar
de Napoles M, Mermoud JE, Wakao R, Tang YA, Endoh M, Appanah R, Nesterova TB, Silva J, Otte AP, Vidal M, Koseki H, Brockdorff N (2004) Polycomb group proteins Ring1A/B link ubiquitylation of histone H2A to heritable gene silencing and X inactivation. Dev Cell 7(5):663–676
PubMed
Article
Google Scholar
Deaton AM, Bird A (2011) CpG islands and the regulation of transcription. Genes Dev 25(10):1010–1022
CAS
PubMed
PubMed Central
Article
Google Scholar
Denissov S, Hofemeister H, Marks H, Kranz A, Ciotta G, Singh S, Anastassiadis K, Stunnenberg HG, Stewart AF (2014) Mll2 is required for H3K4 trimethylation on bivalent promoters in embryonic stem cells, whereas Mll1 is redundant. Development 141(3):526–537
CAS
PubMed
Article
Google Scholar
Devaiah BN, Lewis BA, Cherman N, Hewitt MC, Albrecht BK, Robey PG, Ozato K, Sims RJ, Singer DS (2012) BRD4 is an atypical kinase that phosphorylates serine2 of the RNA polymerase II carboxy-terminal domain. Proc Natl Acad Sci U S A 109(18):6927–6932
CAS
PubMed
PubMed Central
Article
Google Scholar
Dietrich N, Lerdrup M, Landt E, Agrawal-Singh S, Bak M, Tommerup N, Rappsilber J, Sodersten E, Hansen K (2012) REST-mediated recruitment of polycomb repressor complexes in mammalian cells. PLoS Genet 8(3):e1002494
CAS
PubMed
PubMed Central
Article
Google Scholar
Dinger ME, Amaral PP, Mercer TR, Pang KC, Bruce SJ, Gardiner BB, Askarian-Amiri ME, Ru K, Solda G, Simons C, Sunkin SM, Crowe ML, Grimmond SM, Perkins AC, Mattick JS (2008) Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation. Genome Res 18(9):1433–1445
CAS
PubMed
PubMed Central
Article
Google Scholar
Duboule D (2007) The rise and fall of Hox gene clusters. Development 134(14):2549–2560
CAS
PubMed
Article
Google Scholar
Duboule D, Morata G (1994) Colinearity and functional hierarchy among genes of the homeotic complexes. Trends Genet 10(10):358–364
CAS
PubMed
Article
Google Scholar
Enderle D, Beisel C, Stadler MB, Gerstung M, Athri P, Paro R (2011) Polycomb preferentially targets stalled promoters of coding and noncoding transcripts. Genome Res 21(2):216–226
CAS
PubMed
PubMed Central
Article
Google Scholar
Endoh M, Endo TA, Endoh T, Isono K, Sharif J, Ohara O, Toyoda T, Ito T, Eskeland R, Bickmore WA, Vidal M, Bernstein BE, Koseki H (2012) Histone H2A mono-ubiquitination is a crucial step to mediate PRC1-dependent repression of developmental genes to maintain ES cell identity. PLoS Genet 8(7):e1002774
CAS
PubMed
PubMed Central
Article
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(3):452–464
CAS
PubMed
PubMed Central
Article
Google Scholar
Farcas AM, Blackledge NP, Sudbery I, Long HK, McGouran JF, Rose NR, Lee S, Sims D, Cerase A, Sheahan TW, Koseki H, Brockdorff N, Ponting CP, Kessler BM, Klose RJ (2012) KDM2B links the Polycomb Repressive Complex 1 (PRC1) to recognition of CpG islands. Elife 1:e00205
PubMed
PubMed Central
Article
CAS
Google Scholar
Fischle W, Wang Y, Jacobs SA, Kim Y, Allis CD, Khorasanizadeh S (2003) Molecular basis for the discrimination of repressive methyl-lysine marks in histone H3 by Polycomb and HP1 chromodomains. Genes Dev 17(15):1870–1881
CAS
PubMed
PubMed Central
Article
Google Scholar
Fitzgerald DP, Bender W (2001) Polycomb group repression reduces DNA accessibility. Mol Cell Biol 21(19):6585–6597
CAS
PubMed
PubMed Central
Article
Google Scholar
Francis NJ, Kingston RE, Woodcock CL (2004) Chromatin compaction by a polycomb group protein complex. Science 306(5701):1574–1577
CAS
PubMed
Article
Google Scholar
Gambetta MC, Muller J (2014) O-GlcNAcylation prevents aggregation of the Polycomb group repressor polyhomeotic. Dev Cell 31(5):629–639
CAS
PubMed
Article
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(3):344–356
CAS
PubMed
PubMed Central
Article
Google Scholar
Gil J, O’Loghlen A (2014) PRC1 complex diversity: where is it taking us? Trends Cell Biol 24(11):632–641
CAS
PubMed
Article
Google Scholar
Golebiowski FM, Gorecki A, Bonarek P, Rapala-Kozik M, Kozik A, Dziedzicka-Wasylewska M (2012) An investigation of the affinities, specificity and kinetics involved in the interaction between the Yin Yang 1 transcription factor and DNA. FEBS J 279(17):3147–3158
CAS
PubMed
Article
Google Scholar
Grau DJ, Chapman BA, Garlick JD, Borowsky M, Francis NJ, Kingston RE (2011) Compaction of chromatin by diverse Polycomb group proteins requires localized regions of high charge. Genes Dev 25(20):2210–2221
CAS
PubMed
PubMed Central
Article
Google Scholar
Gregory GD, Vakoc CR, Rozovskaia T, Zheng X, Patel S, Nakamura T, Canaani E, Blobel GA (2007) Mammalian ASH1L is a histone methyltransferase that occupies the transcribed region of active genes. Mol Cell Biol 27(24):8466–8479
CAS
PubMed
PubMed Central
Article
Google Scholar
Grossniklaus U, Paro R (2014) Transcriptional silencing by polycomb-group proteins. Cold Spring Harb Perspect Biol 6(11):a019331
PubMed
Article
Google Scholar
Guttman M, Donaghey J, Carey BW, Garber M, Grenier JK, Munson G, Young G, Lucas AB, Ach R, Bruhn L, Yang X, Amit I, Meissner A, Regev A, Rinn JL, Root DE, Lander ES (2011) lincRNAs act in the circuitry controlling pluripotency and differentiation. Nature 477(7364):295–300
CAS
PubMed
PubMed Central
Article
Google Scholar
Hagarman JA, Motley MP, Kristjansdottir K, Soloway PD (2013) Coordinate regulation of DNA methylation and H3K27me3 in mouse embryonic stem cells. PLoS One 8(1):e53880
CAS
PubMed
PubMed Central
Article
Google Scholar
Hajjari M, Behmanesh M, Jahani MM (2014) In silico finding of putative cis-acting elements for the tethering of Polycomb Repressive Complex2 in human genome. Bioinformation 10(4):187–190
PubMed
PubMed Central
Article
Google Scholar
Hansen KH, Bracken AP, Pasini D, Dietrich N, Gehani SS, Monrad A, Rappsilber J, Lerdrup M, Helin K (2008) A model for transmission of the H3K27me3 epigenetic mark. Nat Cell Biol 10(11):1291–1300
CAS
PubMed
Article
Google Scholar
Harrison MM, Botchan MR, Cline TW (2010) Grainyhead and zelda compete for binding to the promoters of the earliest-expressed Drosophila genes. Dev Biol 345(2):248–255
CAS
PubMed
PubMed Central
Article
Google Scholar
Hauenschild A, Ringrose L, Altmutter C, Paro R, Rehmsmeier M (2008) Evolutionary plasticity of polycomb/trithorax response elements in Drosophila species. PLoS Biol 6(10):e261
PubMed
PubMed Central
Article
CAS
Google Scholar
He GP, Kim S, Ro HS (1999) Cloning and characterization of a novel zinc finger transcriptional repressor. A direct role of the zinc finger motif in repression. J Biol Chem 274(21):14678–14684
CAS
PubMed
Article
Google Scholar
He J, Kallin EM, Tsukada Y, Zhang Y (2008) The H3K36 demethylase Jhdm1b/Kdm2b regulates cell proliferation and senescence through p15(Ink4b). Nat Struct Mol Biol 15(11):1169–1175
CAS
PubMed
PubMed Central
Article
Google Scholar
He J, Shen L, Wan M, Taranova O, Wu H, Zhang Y (2013) Kdm2b maintains murine embryonic stem cell status by recruiting PRC1 complex to CpG islands of developmental genes. Nat Cell Biol 15(4):373–384
CAS
PubMed
PubMed Central
Article
Google Scholar
Hekimoglu B, Ringrose L (2009) Non-coding RNAs in polycomb/trithorax regulation. RNA Biol 6(2):129–137
CAS
PubMed
Article
Google Scholar
Hekimoglu-Balkan B, Aszodi A, Heinen R, Jaritz M, Ringrose L (2012) Intergenic Polycomb target sites are dynamically marked by non-coding transcription during lineage commitment. RNA Biol 9(3):314–325
CAS
PubMed
PubMed Central
Article
Google Scholar
Herz HM, Mohan M, Garrett AS, Miller C, Casto D, Zhang Y, Seidel C, Haug JS, Florens L, Washburn MP, Yamaguchi M, Shiekhattar R, Shilatifard A (2012) Polycomb repressive complex 2-dependent and -independent functions of Jarid2 in transcriptional regulation in Drosophila. Mol Cell Biol 32(9):1683–1693
CAS
PubMed
PubMed Central
Article
Google Scholar
Herzog VA, Lempradl A, Trupke J, Okulski H, Altmutter C, Ruge F, Boidol B, Kubicek S, Schmauss G, Aumayr K, et al (2014) A strand-specific switch in noncoding transcription switches the function of a Polycomb/Trithorax response element. Nat Genet
Hodgson JW, Argiropoulos B, Brock HW (2001) Site-specific recognition of a 70-base-pair element containing d(GA)(n) repeats mediates bithoraxoid polycomb group response element-dependent silencing. Mol Cell Biol 21(14):4528–4543
CAS
PubMed
PubMed Central
Article
Google Scholar
Holler M, Westin G, Jiricny J, Schaffner W (1988) Sp1 transcription factor binds DNA and activates transcription even when the binding site is CpG methylated. Genes Dev 2(9):1127–1135
CAS
PubMed
Article
Google Scholar
Hu D, Garruss AS, Gao X, Morgan MA, Cook M, Smith ER, Shilatifard A (2013) The Mll2 branch of the COMPASS family regulates bivalent promoters in mouse embryonic stem cells. Nat Struct Mol Biol 20(9):1093–1097
CAS
PubMed
PubMed Central
Article
Google Scholar
Huang DH, Chang YL (2004) Isolation and characterization of CHRASCH, a polycomb-containing silencing complex. Methods Enzymol 377:267–282
CAS
PubMed
Article
Google Scholar
Huang DH, Chang YL, Yang CC, Pan IC, King B (2002) Pipsqueak encodes a factor essential for sequence-specific targeting of a polycomb group protein complex. Mol Cell Biol 22(17):6261–6271
CAS
PubMed
PubMed Central
Article
Google Scholar
Hunkapiller J, Shen Y, Diaz A, Cagney G, McCleary D, Ramalho-Santos M, Krogan N, Ren B, Song JS, Reiter JF (2012) Polycomb-like 3 promotes polycomb repressive complex 2 binding to CpG islands and embryonic stem cell self-renewal. PLoS Genet 8(3):e1002576
CAS
PubMed
PubMed Central
Article
Google Scholar
Illingworth RS, Gruenewald-Schneider U, Webb S, Kerr AR, James KD, Turner DJ, Smith C, Harrison DJ, Andrews R, Bird AP (2010) Orphan CpG islands identify numerous conserved promoters in the mammalian genome. PLoS Genet 6(9):e1001134
PubMed
PubMed Central
Article
CAS
Google Scholar
Jermann P, Hoerner L, Burger L, Schubeler D (2014) Short sequences can efficiently recruit histone H3 lysine 27 trimethylation in the absence of enhancer activity and DNA methylation. Proc Natl Acad Sci U S A 111(33):E3415–E3421
CAS
PubMed
PubMed Central
Article
Google Scholar
Jothi R, Cuddapah S, Barski A, Cui K, Zhao K (2008) Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data. Nucleic Acids Res 36(16):5221–5231
CAS
PubMed
PubMed Central
Article
Google Scholar
Jung HR, Pasini D, Helin K, Jensen ON (2010) Quantitative mass spectrometry of histones H3.2 and H3.3 in Suz12-deficient mouse embryonic stem cells reveals distinct, dynamic post-translational modifications at Lys-27 and Lys-36. Mol Cell Proteomics 9(5):838–850
CAS
PubMed
PubMed Central
Article
Google Scholar
Kalb R, Latwiel S, Baymaz HI, Jansen PW, Muller CW, Vermeulen M, Muller J (2014) Histone H2A monoubiquitination promotes histone H3 methylation in Polycomb repression. Nat Struct Mol Biol 21(6):569–571
CAS
PubMed
Article
Google Scholar
Kaneko S, Li G, Son J, Xu CF, Margueron R, Neubert TA, Reinberg D (2010) Phosphorylation of the PRC2 component Ezh2 is cell cycle-regulated and up-regulates its binding to ncRNA. Genes Dev 24(23):2615–2620
CAS
PubMed
PubMed Central
Article
Google Scholar
Kaneko S, Son J, Bonasio R, Shen SS, Reinberg D (2014) Nascent RNA interaction keeps PRC2 activity poised and in check. Genes Dev 28(18):1983–1988
CAS
PubMed
PubMed Central
Article
Google Scholar
Kassis JA (1994) Unusual properties of regulatory DNA from the Drosophila engrailed gene: three “pairing-sensitive” sites within a 1.6-kb region. Genetics 136(3):1025–1038
CAS
PubMed
PubMed Central
Google Scholar
Kassis JA, Brown JL (2013) Polycomb group response elements in Drosophila and vertebrates. Adv Genet 81:83–118
CAS
PubMed
PubMed Central
Article
Google Scholar
Kellner WA, Van Bortle K, Li L, Ramos E, Takenaka N, Corces VG (2013) Distinct isoforms of the Drosophila Brd4 homologue are present at enhancers, promoters and insulator sites. Nucleic Acids Res 41(20):9274–9283
CAS
PubMed
PubMed Central
Article
Google Scholar
Kennison JA (2004) Introduction to Trx-G and Pc-G genes. Methods Enzymol 377:61–70
CAS
PubMed
Article
Google Scholar
Kherrouche Z, Begue A, Stehelin D, Monte D (2001) Molecular cloning and characterization of the mouse E2F6 gene. Biochem Biophys Res Commun 288(1):22–33
CAS
PubMed
Article
Google Scholar
Kim J, Kim J (2009) YY1’s longer DNA-binding motifs. Genomics 93(2):152–158
CAS
PubMed
Article
Google Scholar
Kim CG, Swendeman SL, Barnhart KM, Sheffery M (1990) Promoter elements and erythroid cell nuclear factors that regulate alpha-globin gene transcription in vitro. Mol Cell Biol 10(11):5958–5966
CAS
PubMed
PubMed Central
Article
Google Scholar
Kim CA, Gingery M, Pilpa RM, Bowie JU (2002) The SAM domain of polyhomeotic forms a helical polymer. Nat Struct Biol 9(6):453–457
CAS
PubMed
Google Scholar
Kim CA, Sawaya MR, Cascio D, Kim W, Bowie JU (2005) Structural organization of a Sex-comb-on-midleg/polyhomeotic copolymer. J Biol Chem 280(30):27769–27775
CAS
PubMed
Article
Google Scholar
Kim H, Kang K, Kim J (2009) AEBP2 as a potential targeting protein for polycomb repression complex PRC2. Nucleic Acids Res 37(9):2940–2950
CAS
PubMed
PubMed Central
Article
Google Scholar
Kingston RE, Tamkun JW (2014) Transcriptional regulation by trithorax-group proteins. Cold Spring Harb Perspect Biol 6(10):a019349
PubMed
Article
CAS
Google Scholar
Klose RJ, Cooper S, Farcas AM, Blackledge NP, Brockdorff N (2013) Chromatin sampling–an emerging perspective on targeting polycomb repressor proteins. PLoS Genet 9(8):e1003717
CAS
PubMed
PubMed Central
Article
Google Scholar
Kozma G, Bender W, Sipos L (2008) Replacement of a Drosophila Polycomb response element core, and in situ analysis of its DNA motifs. Mol Gen Genomics 279(6):595–603
CAS
Article
Google Scholar
Krajewski WA, Nakamura T, Mazo A, Canaani E (2005) A motif within SET-domain proteins binds single-stranded nucleic acids and transcribed and supercoiled DNAs and can interfere with assembly of nucleosomes. Mol Cell Biol 25(5):1891–1899
CAS
PubMed
PubMed Central
Article
Google Scholar
Krebs AR, Dessus-Babus S, Burger L, Schubeler D (2014) High-throughput engineering of a mammalian genome reveals building principles of methylation states at CG rich regions. Elife 3:e04094
PubMed
PubMed Central
Article
CAS
Google Scholar
Ku M, Koche RP, Rheinbay E, Mendenhall EM, Endoh M, Mikkelsen TS, Presser A, Nusbaum C, Xie X, Chi AS, Adli M, Kasif S, Ptaszek LM, Cowan CA, Lander ES, Koseki H, Bernstein BE (2008) Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains. PLoS Genet 4(10):e1000242
PubMed
PubMed Central
Article
CAS
Google Scholar
Kuzmichev A, Nishioka K, Erdjument-Bromage H, Tempst P, Reinberg D (2002) Histone methyltransferase activity associated with a human multiprotein complex containing the Enhancer of Zeste protein. Genes Dev 16(22):2893–2905
CAS
PubMed
PubMed Central
Article
Google Scholar
Kuzmichev A, Jenuwein T, Tempst P, Reinberg D (2004) Different EZH2-containing complexes target methylation of histone H1 or nucleosomal histone H3. Mol Cell 14(2):183–193
CAS
PubMed
Article
Google Scholar
Kyba M, Brock HW (1998) The SAM domain of polyhomeotic, RAE28, and scm mediates specific interactions through conserved residues. Dev Genet 22(1):74–84
CAS
PubMed
Article
Google Scholar
Lagarou A, Mohd-Sarip A, Moshkin YM, Chalkley GE, Bezstarosti K, Demmers JA, Verrijzer CP (2008) dKDM2 couples histone H2A ubiquitylation to histone H3 demethylation during Polycomb group silencing. Genes Dev 22(20):2799–2810
CAS
PubMed
PubMed Central
Article
Google Scholar
Laible G, Wolf A, Dorn R, Reuter G, Nislow C, Lebersorger A, Popkin D, Pillus L, Jenuwein T (1997) Mammalian homologues of the Polycomb-group gene Enhancer of zeste mediate gene silencing in Drosophila heterochromatin and at S. cerevisiae telomeres. EMBO J 16(11):3219–3232
CAS
PubMed
PubMed Central
Article
Google Scholar
Lan F, Bayliss PE, Rinn JL, Whetstine JR, Wang JK, Chen S, Iwase S, Alpatov R, Issaeva I, Canaani E, Roberts TM, Chang HY, Shi Y (2007) A histone H3 lysine 27 demethylase regulates animal posterior development. Nature 449(7163):689–694
CAS
PubMed
Article
Google Scholar
Landeira D, Sauer S, Poot R, Dvorkina M, Mazzarella L, Jorgensen HF, Pereira CF, Leleu M, Piccolo FM, Spivakov M, Brookes E, Pombo A, Fisher C, Skarnes WC, Snoek T, Bezstarosti K, Demmers J, Klose RJ, Casanova M, Tavares L, Brockdorff N, Merkenschlager M, Fisher AG (2010) Jarid2 is a PRC2 component in embryonic stem cells required for multi-lineage differentiation and recruitment of PRC1 and RNA Polymerase II to developmental regulators. Nat Cell Biol 12(6):618–624
CAS
PubMed
PubMed Central
Article
Google Scholar
Lanzuolo C, Orlando V (2012) Memories from the Polycomb group proteins. Annu Rev Genet 46:561–589
CAS
PubMed
Article
Google Scholar
Lehmann L, Ferrari R, Vashisht AA, Wohlschlegel JA, Kurdistani SK, Carey M (2012) Polycomb repressive complex 1 (PRC1) disassembles RNA polymerase II preinitiation complexes. J Biol Chem 287(43):35784–35794
CAS
PubMed
PubMed Central
Article
Google Scholar
Li G, Margueron R, Ku M, Chambon P, Bernstein BE, Reinberg D (2010) Jarid2 and PRC2, partners in regulating gene expression. Genes Dev 24(4):368–380
PubMed
PubMed Central
Article
CAS
Google Scholar
Lo SM, Ahuja NK, Francis NJ (2009) Polycomb group protein Suppressor 2 of Zeste is a functional homolog of posterior sex combs. Mol Cell Biol 29(2):515–525
CAS
PubMed
Article
Google Scholar
Long HK, Blackledge NP, Klose RJ (2013a) ZF-CxxC domain-containing proteins, CpG islands and the chromatin connection. Biochem Soc Trans 41(3):727–740
CAS
PubMed
PubMed Central
Article
Google Scholar
Long HK, Sims D, Heger A, Blackledge NP, Kutter C, Wright ML, Grützner F, Odom DT, Patient R, Ponting CP, Klose RJ (2013b) Epigenetic conservation at gene regulatory elements revealed by non-methylated DNA profiling in seven vertebrates. Elife 2:e00348
PubMed
PubMed Central
Article
Google Scholar
Lynch MD, Smith AJ, De Gobbi M, Flenley M, Hughes JR, Vernimmen D, Ayyub H, Sharpe JA, Sloane-Stanley JA, Sutherland L, Meek S, Burdon T, Gibbons RJ, Garrick D, Higgs DR (2012) An interspecies analysis reveals a key role for unmethylated CpG dinucleotides in vertebrate Polycomb complex recruitment. EMBO J 31(2):317–329
CAS
PubMed
Article
Google Scholar
Mace KA, Pearson JC, McGinnis W (2005) An epidermal barrier wound repair pathway in Drosophila is mediated by grainy head. Science 308(5720):381–385
CAS
PubMed
Article
Google Scholar
Maeda RK, Karch F (2006) The ABC of the BX-C: the bithorax complex explained. Development 133(8):1413–1422
CAS
PubMed
Article
Google Scholar
Maeda RK, Karch F (2009) The bithorax complex of Drosophila an exceptional Hox cluster. Curr Top Dev Biol 88:1–33
CAS
PubMed
Article
Google Scholar
Margueron R, Reinberg D (2011) The Polycomb complex PRC2 and its mark in life. Nature 469(7330):343–349
CAS
PubMed
PubMed Central
Article
Google Scholar
Margueron R, Li G, Sarma K, Blais A, Zavadil J, Woodcock CL, Dynlacht BD, Reinberg D (2008) Ezh1 and Ezh2 maintain repressive chromatin through different mechanisms. Mol Cell 32(4):503–518
CAS
PubMed
PubMed Central
Article
Google Scholar
Margueron R, Justin N, Ohno K, Sharpe ML, Son J, Drury WJ 3rd, Voigt P, Martin SR, Taylor WR, De Marco V, Pirrotta V, Reinberg D, Gamblin SJ (2009) Role of the polycomb protein EED in the propagation of repressive histone marks. Nature 461(7265):762–767
CAS
PubMed
PubMed Central
Article
Google Scholar
Matharu NK, Hussain T, Sankaranarayanan R, Mishra RK (2010) Vertebrate homologue of Drosophila GAGA factor. J Mol Biol 400(3):434–447
CAS
PubMed
Article
Google Scholar
Mazzoni EO, Mahony S, Peljto M, Patel T, Thornton SR, McCuine S, Reeder C, Boyer LA, Young RA, Gifford DK, Wichterle H (2013) Saltatory remodeling of Hox chromatin in response to rostrocaudal patterning signals. Nat Neurosci 16(9):1191–1198
CAS
PubMed
PubMed Central
Article
Google Scholar
McCall K, Bender W (1996) Probes of chromatin accessibility in the Drosophila bithorax complex respond differently to Polycomb-mediated repression. EMBO J 15(3):569–580
CAS
PubMed
PubMed Central
Google Scholar
Mendenhall EM, Koche RP, Truong T, Zhou VW, Issac B, Chi AS, Ku M, Bernstein BE (2010) GC-rich sequence elements recruit PRC2 in mammalian ES cells. PLoS Genet 6(12):e1001244
PubMed
PubMed Central
Article
CAS
Google Scholar
Meng S, Luo M, Sun H, Yu X, Shen M, Zhang Q, Zhou R, Ju X, Tao W, Liu D, Deng H, Lu Z (2010) Identification and characterization of Bmi-1-responding element within the human p16 promoter. J Biol Chem 285(43):33219–33229
CAS
PubMed
PubMed Central
Article
Google Scholar
Mihaly J, Mishra RK, Karch F (1998) A conserved sequence motif in Polycomb-response elements. Mol Cell 1(7):1065–1066
CAS
PubMed
Article
Google Scholar
Min J, Zhang Y, Xu RM (2003) Structural basis for specific binding of Polycomb chromodomain to histone H3 methylated at Lys 27. Genes Dev 17(15):1823–1828
CAS
PubMed
PubMed Central
Article
Google Scholar
Morey L, Pascual G, Cozzuto L, Roma G, Wutz A, Benitah SA, Di Croce L (2012) Nonoverlapping functions of the Polycomb group CBX family of proteins in embryonic stem cells. Cell Stem Cell 10(1):47–62
CAS
PubMed
Article
Google Scholar
Mousavi K, Zare H, Wang AH, Sartorelli V (2012) Polycomb protein Ezh1 promotes RNA polymerase II elongation. Mol Cell 45(2):255–262
CAS
PubMed
Article
Google Scholar
Muller J, Gaunt S, Lawrence PA (1995) Function of the Polycomb protein is conserved in mice and flies. Development 121(9):2847–2852
CAS
PubMed
Google Scholar
Muller J, Hart CM, Francis NJ, Vargas ML, Sengupta A, Wild B, Miller EL, O’Connor MB, Kingston RE, Simon JA (2002) Histone methyltransferase activity of a Drosophila Polycomb group repressor complex. Cell 111(2):197–208
CAS
PubMed
Article
Google Scholar
Niessen HE, Demmers JA, Voncken JW (2009) Talking to chromatin: post-translational modulation of polycomb group function. Epigenetics Chromatin 2(1):10
PubMed
PubMed Central
Article
CAS
Google Scholar
Noordermeer D, Duboule D (2013) Chromatin architectures and Hox gene collinearity. Curr Top Dev Biol 104:113–148
CAS
PubMed
Article
Google Scholar
Ogawa H, Ishiguro K, Gaubatz S, Livingston DM, Nakatani Y (2002) A complex with chromatin modifiers that occupies E2F- and Myc-responsive genes in G0 cells. Science 296(5570):1132–1136
CAS
PubMed
Article
Google Scholar
Okulski H, Druck B, Bhalerao S, Ringrose L (2011) Quantitative analysis of polycomb response elements (PREs) at identical genomic locations distinguishes contributions of PRE sequence and genomic environment. Epigenetics Chromatin 4:4
CAS
PubMed
PubMed Central
Article
Google Scholar
O’Loghlen A, Munoz-Cabello AM, Gaspar-Maia A, Wu HA, Banito A, Kunowska N, Racek T, Pemberton HN, Beolchi P, Lavial F, Masui O, Vermeulen M, Carroll T, Graumann J, Heard E, Dillon N, Azuara V, Snijders AP, Peters G, Bernstein E, Gil J (2012) MicroRNA regulation of CBX7 mediates a switch of Polycomb orthologs during ESC differentiation. Cell Stem Cell 10(1):33–46
PubMed
PubMed Central
Article
CAS
Google Scholar
Orlando V, Jane EP, Chinwalla V, Harte PJ, Paro R (1998) Binding of trithorax and Polycomb proteins to the bithorax complex: dynamic changes during early Drosophila embryogenesis. EMBO J 17(17):5141–5150
CAS
PubMed
PubMed Central
Article
Google Scholar
Ost A, Lempradl A, Casas E, Weigert M, Tiko T, Deniz M, Pantano L, Boenisch U, Itskov PM, Stoeckius M, Ruf M, Rajewsky N, Reuter G, Iovino N, Ribeiro C, Alenius M, Heyne S, Vavouri T, Pospisilik JA (2014) Paternal diet defines offspring chromatin state and intergenerational obesity. Cell 159(6):1352–1364
PubMed
Article
CAS
Google Scholar
Pasini D, Cloos PA, Walfridsson J, Olsson L, Bukowski JP, Johansen JV, Bak M, Tommerup N, Rappsilber J, Helin K (2010a) JARID2 regulates binding of the Polycomb repressive complex 2 to target genes in ES cells. Nature 464(7286):306–310
CAS
PubMed
Article
Google Scholar
Pasini D, Malatesta M, Jung HR, Walfridsson J, Willer A, Olsson L, Skotte J, Wutz A, Porse B, Jensen ON, Helin K (2010b) 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
CAS
PubMed
PubMed Central
Article
Google Scholar
Patsialou A, Wilsker D, Moran E (2005) DNA-binding properties of ARID family proteins. Nucleic Acids Res 33(1):66–80
CAS
PubMed
PubMed Central
Article
Google Scholar
Pedone PV, Ghirlando R, Clore GM, Gronenborn AM, Felsenfeld G, Omichinski JG (1996) The single Cys2-His2 zinc finger domain of the GAGA protein flanked by basic residues is sufficient for high-affinity specific DNA binding. Proc Natl Acad Sci U S A 93(7):2822–2826
CAS
PubMed
PubMed Central
Article
Google Scholar
Pemberton H, Anderton E, Patel H, Brookes S, Chandler H, Palermo R, Stock J, Rodriguez-Niedenführ M, Racek T, de Breed L, Stewart A, Matthews N, Peters G (2014) Genome-wide co-localization of Polycomb orthologs and their effects on gene expression in human fibroblasts. Genome Biol 15(2):R23
PubMed
PubMed Central
Article
CAS
Google Scholar
Peng JC, Valouev A, Swigut T, Zhang J, Zhao Y, Sidow A, Wysocka J (2009) Jarid2/Jumonji coordinates control of PRC2 enzymatic activity and target gene occupancy in pluripotent cells. Cell 139(7):1290–1302
PubMed
PubMed Central
Article
Google Scholar
Perez L, Barrio L, Cano D, Fiuza UM, Muzzopappa M, Milan M (2011) Enhancer-PRE communication contributes to the expansion of gene expression domains in proliferating primordia. Development 138(15):3125–3134
CAS
PubMed
Article
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(5):922–933
CAS
PubMed
PubMed Central
Article
Google Scholar
Pirrotta V, Li HB (2012) A view of nuclear Polycomb bodies. Curr Opin Genet Dev 22(2):101–109
CAS
PubMed
Article
Google Scholar
Poux S, McCabe D, Pirrotta V (2001) Recruitment of Polycomb group chromatin complexes in Drosophila. Development 128(1):75–85
CAS
PubMed
Google Scholar
Reddington JP, Perricone SM, Nestor CE, Reichmann J, Youngson NA, Suzuki M, Reinhardt D, Dunican DS, Prendergast JG, Mjoseng H, Ramsahoye BH, Whitelaw E, Greally JM, Adams IR, Bickmore WA, Meehan RR (2013) Redistribution of H3K27me3 upon DNA hypomethylation results in de-repression of Polycomb target genes. Genome Biol 14(3):R25
PubMed
PubMed Central
Article
CAS
Google Scholar
Ren X, Kerppola TK (2011) REST interacts with CBX proteins and regulates polycomb repressive complex 1 occupancy at RE1 elements. Mol Cell Biol 31(10):2100–2110
CAS
PubMed
PubMed Central
Article
Google Scholar
Richly H, Aloia L, Di Croce L (2011) Roles of the Polycomb group proteins in stem cells and cancer. Cell Death Dis 2:e204
CAS
PubMed
PubMed Central
Article
Google Scholar
Riising EM, Comet I, Leblanc B, Wu X, Johansen JV, Helin K (2014) Gene silencing triggers polycomb repressive complex 2 recruitment to CpG islands genome wide. Mol Cell 55(3):347–360
CAS
PubMed
Article
Google Scholar
Ringrose L (2007) Polycomb comes of age: genome-wide profiling of target sites. Curr Opin Cell Biol 19(3):290–297
CAS
PubMed
Article
Google Scholar
Ringrose L, Paro R (2004) Epigenetic regulation of cellular memory by the Polycomb and Trithorax group proteins. Annu Rev Genet 38(1):413–443
CAS
PubMed
Article
Google Scholar
Ringrose L, Paro R (2007) Polycomb/Trithorax response elements and epigenetic memory of cell identity. Development 134(2):223–232
CAS
PubMed
Article
Google Scholar
Ringrose L, Rehmsmeier M, Dura JM, Paro R (2003) Genome-wide prediction of Polycomb/Trithorax response elements in Drosophila melanogaster. Dev Cell 5(5):759–771
CAS
PubMed
Article
Google Scholar
Robinson AK, Leal BZ, Chadwell LV, Wang R, Ilangovan U, Kaur Y, Junco SE, Schirf V, Osmulski PA, Gaczynska M, Hinck AP, Demeler B, McEwen DG, Kim CA (2012) The growth-suppressive function of the polycomb group protein polyhomeotic is mediated by polymerization of its sterile alpha motif (SAM) domain. J Biol Chem 287(12):8702–8713
CAS
PubMed
PubMed Central
Article
Google Scholar
Rozovskaia T, Tillib S, Smith S, Sedkov Y, Rozenblatt-Rosen O, Petruk S, Yano T, Nakamura T, Ben-Simchon L, Gildea J, Croce CM, Shearn A, Canaani E, Mazo A (1999) Trithorax and ASH1 interact directly and associate with the trithorax group-responsive bxd region of the ultrabithorax promoter. Mol Cell Biol 19(9):6441–6447
CAS
PubMed
PubMed Central
Article
Google Scholar
Sanchez C, Sanchez I, Demmers JA, Rodriguez P, Strouboulis J, Vidal M (2007) Proteomics analysis of Ring1B/Rnf2 interactors identifies a novel complex with the Fbxl10/Jhdm1B histone demethylase and the Bcl6 interacting corepressor. Mol Cell Proteomics 6(5):820–834
CAS
PubMed
Article
Google Scholar
Sanulli S, Justin N, Teissandier A, Ancelin K, Portoso M, Caron M, Michaud A, Lombard B, da Rocha ST, Offer J, Loew D, Servant N, Wassef M, Burlina F, Gamblin SJ, Heard E, Margueron R (2015) Jarid2 methylation via the PRC2 complex regulates H3K27me3 deposition during cell differentiation. Mol Cell 57(5):769–783
CAS
PubMed
PubMed Central
Article
Google Scholar
Sasai N, Kato Y, Kimura G, Takeuchi T, Yamaguchi M (2007) The Drosophila jumonji gene encodes a JmjC-containing nuclear protein that is required for metamorphosis. FEBS J 274(23):6139–6151
CAS
PubMed
Article
Google Scholar
Scheuermann JC, Gutierrez L, Muller J (2012) Histone H2A monoubiquitination and Polycomb repression: the missing pieces of the puzzle. Fly 6(3):162–168
CAS
PubMed
Article
Google Scholar
Schmitges FW, Prusty AB, Faty M, Stutzer A, Lingaraju GM, Aiwazian J, Sack R, Hess D, Li L, Zhou S, Bunker RD, Wirth U, Bouwmeester T, Bauer A, Ly-Hartig N, Zhao K, Chan H, Gu J, Gut H, Fischle W, Muller J, Thoma NH (2011) Histone methylation by PRC2 is inhibited by active chromatin marks. Mol Cell 42(3):330–341
CAS
PubMed
Article
Google Scholar
Schoeftner S, Sengupta AK, Kubicek S, Mechtler K, Spahn L, Koseki H, Jenuwein T, Wutz A (2006) Recruitment of PRC1 function at the initiation of X inactivation independent of PRC2 and silencing. EMBO J 25(13):3110–3122
CAS
PubMed
PubMed Central
Article
Google Scholar
Schoenherr CJ, Anderson DJ (1995) The neuron-restrictive silencer factor (NRSF): a coordinate repressor of multiple neuron-specific genes. Science 267(5202):1360–1363
CAS
PubMed
Article
Google Scholar
Schorderet P, Lonfat N, Darbellay F, Tschopp P, Gitto S, Soshnikova N, Duboule D (2013) A genetic approach to the recruitment of PRC2 at the HoxD locus. PLoS Genet 9(11):e1003951
PubMed
PubMed Central
Article
CAS
Google Scholar
Schuettengruber B, Chourrout D, Vervoort M, Leblanc B, Cavalli G (2007) Genome regulation by polycomb and trithorax proteins. Cell 128(4):735–745
CAS
PubMed
Article
Google Scholar
Schuettengruber B, Ganapathi M, Leblanc B, Portoso M, Jaschek R, Tolhuis B, van Lohuizen M, Tanay A, Cavalli G (2009) Functional anatomy of polycomb and trithorax chromatin landscapes in Drosophila embryos. PLoS Biol 7(1):e13
PubMed
Article
CAS
Google Scholar
Schuettengruber B, Oded Elkayam N, Sexton T, Entrevan M, Stern S, Thomas A, Yaffe E, Parrinello H, Tanay A, Cavalli G (2014) Cooperativity, specificity, and evolutionary stability of polycomb targeting in Drosophila. Cell Rep 9(1):219–233
CAS
PubMed
Article
Google Scholar
Sedaghat Y, Miranda WF, Sonnenfeld MJ (2002) The jing Zn-finger transcription factor is a mediator of cellular differentiation in the Drosophila CNS midline and trachea. Development 129(11):2591–2606
CAS
PubMed
Google Scholar
Shen X, Liu Y, Hsu YJ, Fujiwara Y, Kim J, Mao X, Yuan GC, Orkin SH (2008) EZH1 mediates methylation on histone H3 lysine 27 and complements EZH2 in maintaining stem cell identity and executing pluripotency. Mol Cell 32(4):491–502
CAS
PubMed
PubMed Central
Article
Google Scholar
Shen X, Kim W, Fujiwara Y, Simon MD, Liu Y, Mysliwiec MR, Yuan GC, Lee Y, Orkin SH (2009) Jumonji modulates polycomb activity and self-renewal versus differentiation of stem cells. Cell 139(7):1303–1314
PubMed
PubMed Central
Article
Google Scholar
Simon JA, Kingston RE (2009) Mechanisms of polycomb gene silencing: knowns and unknowns. Nat Rev Mol Cell Biol 10(10):697–708
CAS
PubMed
Article
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(5):808–824
CAS
PubMed
PubMed Central
Article
Google Scholar
Simon J, Chiang A, Bender W, Shimell MJ, O’Connor M (1993) Elements of the Drosophila bithorax complex that mediate repression by Polycomb group products. Dev Biol 158(1):131–144
CAS
PubMed
Article
Google Scholar
Sing A, Pannell D, Karaiskakis A, Sturgeon K, Djabali M, Ellis J, Lipshitz HD, Cordes SP (2009) A vertebrate polycomb response element governs segmentation of the posterior hindbrain. Cell 138(5):885–897
CAS
PubMed
Article
Google Scholar
Smigova J, Juda P, Krejci J, Raska I (2014) Structural basis of polycomb bodies. Folia Biol (Praha) 60(Suppl 1):13–20
Google Scholar
Soshnikova N, Duboule D (2009a) Epigenetic regulation of vertebrate Hox genes: a dynamic equilibrium. Epigenetics 4(8):537–540
CAS
PubMed
Article
Google Scholar
Soshnikova N, Duboule D (2009b) Epigenetic temporal control of mouse Hox genes in vivo. Science 324(5932):1320–1323
CAS
PubMed
Article
Google Scholar
Squazzo SL, O’Geen H, Komashko VM, Krig SR, Jin VX, Jang SW, Margueron R, Reinberg D, Green R, Farnham PJ (2006) Suz12 binds to silenced regions of the genome in a cell-type-specific manner. Genome Res 16(7):890–900
CAS
PubMed
PubMed Central
Article
Google Scholar
Srinivasan L, Pan X, Atchison ML (2005) Transient requirements of YY1 expression for PcG transcriptional repression and phenotypic rescue. J Cell Biochem 96(4):689–699
CAS
PubMed
Article
Google Scholar
Srivastava S, Puri D, Garapati HS, Dhawan J, Mishra RK (2013) Vertebrate GAGA factor associated insulator elements demarcate homeotic genes in the HOX clusters. Epigenetics Chromatin 6(1):8
CAS
PubMed
PubMed Central
Article
Google Scholar
Steffen PA, Ringrose L (2014) What are memories made of? How Polycomb and Trithorax proteins mediate epigenetic memory. Nat Rev Mol Cell Biol 15(5):340–356
CAS
PubMed
Article
Google Scholar
Stock JK, Giadrossi S, Casanova M, Brookes E, Vidal M, Koseki H, Brockdorff N, Fisher AG, Pombo A (2007) Ring1-mediated ubiquitination of H2A restrains poised RNA polymerase II at bivalent genes in mouse ES cells. Nat Cell Biol 9(12):1428–1435
CAS
PubMed
Article
Google Scholar
Stojic L, Jasencakova Z, Prezioso C, Stutzer A, Bodega B, Pasini D, Klingberg R, Mozzetta C, Margueron R, Puri PL, Schwarzer D, Helin K, Fischle W, Orlando V (2011) Chromatin regulated interchange between polycomb repressive complex 2 (PRC2)-Ezh2 and PRC2-Ezh1 complexes controls myogenin activation in skeletal muscle cells. Epigenetics Chromatin 4:16
CAS
PubMed
PubMed Central
Article
Google Scholar
Stros M (2010) HMGB proteins: interactions with DNA and chromatin. Biochim Biophys Acta 1799(1–2):101–113
CAS
PubMed
Article
Google Scholar
Tanaka Y, Katagiri Z, Kawahashi K, Kioussis D, Kitajima S (2007) Trithorax-group protein ASH1 methylates histone H3 lysine 36. Gene 397(1–2):161–168
CAS
PubMed
Article
Google Scholar
Tanay A, O’Donnell AH, Damelin M, Bestor TH (2007) Hyperconserved CpG domains underlie Polycomb-binding sites. Proc Natl Acad Sci U S A 104(13):5521–5526
CAS
PubMed
PubMed Central
Article
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(7291):1082–1086
CAS
PubMed
PubMed Central
Article
Google Scholar
Tie F, Banerjee R, Stratton CA, Prasad-Sinha J, Stepanik V, Zlobin A, Diaz MO, Scacheri PC, Harte PJ (2009) CBP-mediated acetylation of histone H3 lysine 27 antagonizes Drosophila polycomb silencing. Development 136(18):3131–3141
CAS
PubMed
PubMed Central
Article
Google Scholar
Tie F, Banerjee R, Conrad PA, Scacheri PC, Harte PJ (2012) Histone demethylase UTX and chromatin remodeler BRM bind directly to CBP and modulate acetylation of histone H3 lysine 27. Mol Cell Biol 32(12):2323–2334
CAS
PubMed
PubMed Central
Article
Google Scholar
Tie F, Banerjee R, Saiakhova AR, Howard B, Monteith KE, Scacheri PC, Cosgrove MS, Harte PJ (2014) Trithorax monomethylates histone H3K4 and interacts directly with CBP to promote H3K27 acetylation and antagonize Polycomb silencing. Development 141(5):1129–1139
CAS
PubMed
PubMed Central
Article
Google Scholar
Trimarchi JM, Fairchild B, Wen J, Lees JA (2001) The E2F6 transcription factor is a component of the mammalian Bmi1-containing polycomb complex. Proc Natl Acad Sci U S A 98(4):1519–1524
CAS
PubMed
PubMed Central
Article
Google Scholar
Trojer P, Cao AR, Gao Z, Li Y, Zhang J, Xu X, Li G, Losson R, Erdjument-Bromage H, Tempst P, Farnham PJ, Reinberg D (2011) L3MBTL2 protein acts in concert with PcG protein-mediated monoubiquitination of H2A to establish a repressive chromatin structure. Mol Cell 42(4):438–450
CAS
PubMed
PubMed Central
Article
Google Scholar
Tsuda L, Kaido M, Lim YM, Kato K, Aigaki T, Hayashi S (2006) An NRSF/REST-like repressor downstream of Ebi/SMRTER/Su(H) regulates eye development in Drosophila. EMBO J 25(13):3191–3202
CAS
PubMed
PubMed Central
Article
Google Scholar
Uv AE, Thompson CR, Bray SJ (1994) The Drosophila tissue-specific factor Grainyhead contains novel DNA-binding and dimerization domains which are conserved in the human protein CP2. Mol Cell Biol 14(6):4020–4031
CAS
PubMed
PubMed Central
Article
Google Scholar
van Heeringen SJ, Akkers RC, van Kruijsbergen I, Arif MA, Hanssen LL, Sharifi N, Veenstra GJ (2014) Principles of nucleation of H3K27 methylation during embryonic development. Genome Res 24(3):401–410
PubMed
PubMed Central
Article
CAS
Google Scholar
Vasanthi D, Nagabhushan A, Matharu NK, Mishra RK (2013) A functionally conserved Polycomb response element from mouse HoxD complex responds to heterochromatin factors. Sci Rep 3:3011
PubMed
PubMed Central
Article
Google Scholar
Wachter E, Quante T, Merusi C, Arczewska A, Stewart F, Webb S, Bird A (2014) Synthetic CpG islands reveal DNA sequence determinants of chromatin structure. Elife 3:e03397
PubMed
PubMed Central
Article
CAS
Google Scholar
Walker E, Chang WY, Hunkapiller J, Cagney G, Garcha K, Torchia J, Krogan NJ, Reiter JF, Stanford WL (2010) Polycomb-like 2 associates with PRC2 and regulates transcriptional networks during mouse embryonic stem cell self-renewal and differentiation. Cell Stem Cell 6(2):153–166
CAS
PubMed
PubMed Central
Article
Google Scholar
Wang H, Wang L, Erdjument-Bromage H, Vidal M, Tempst P, Jones RS, Zhang Y (2004a) Role of histone H2A ubiquitination in polycomb silencing. Nature 431(7010):873–878
CAS
PubMed
Article
Google Scholar
Wang L, Brown JL, Cao R, Zhang Y, Kassis JA, Jones RS (2004b) Hierarchical recruitment of polycomb group silencing complexes. Mol Cell 14(5):637–646
CAS
PubMed
Article
Google Scholar
Wang KC, Yang YW, Liu B, Sanyal A, Corces-Zimmerman R, Chen Y, Lajoie BR, Protacio A, Flynn RA, Gupta RA, Wysocka J, Lei M, Dekker J, Helms JA, Chang HY (2011) A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression. Nature 472(7341):120–124
CAS
PubMed
PubMed Central
Article
Google Scholar
Wildonger J, Sosinsky A, Honig B, Mann RS (2005) Lozenge directly activates argos and klumpfuss to regulate programmed cell death. Genes Dev 19(9):1034–1039
CAS
PubMed
PubMed Central
Article
Google Scholar
Wilkinson FH, Park K, Atchison ML (2006) Polycomb recruitment to DNA in vivo by the YY1 REPO domain. Proc Natl Acad Sci U S A 103(51):19296–19301
CAS
PubMed
PubMed Central
Article
Google Scholar
Woo CJ, Kharchenko PV, Daheron L, Park PJ, Kingston RE (2010) A region of the human HOXD cluster that confers polycomb-group responsiveness. Cell 140(1):99–110
CAS
PubMed
PubMed Central
Article
Google Scholar
Woo CJ, Kharchenko PV, Daheron L, Park PJ, Kingston RE (2013) Variable requirements for DNA-binding proteins at polycomb-dependent repressive regions in human HOX clusters. Mol Cell Biol 33(16):3274–3285
CAS
PubMed
PubMed Central
Article
Google Scholar
Wu X, Johansen JV, Helin K (2013) Fbxl10/Kdm2b recruits polycomb repressive complex 1 to CpG islands and regulates H2A ubiquitylation. Mol Cell 49(6):1134–1146
CAS
PubMed
Article
Google Scholar
Xu J, Shao Z, Li D, Xie H, Kim W, Huang J, Taylor JE, Pinello L, Glass K, Jaffe JD, Yuan GC, Orkin SH (2015) Developmental control of polycomb subunit composition by GATA factors mediates a switch to non-canonical functions. Mol Cell 57(2):304–316
CAS
PubMed
PubMed Central
Article
Google Scholar
Yap KL, Li S, Munoz-Cabello AM, Raguz S, Zeng L, Mujtaba S, Gil J, Walsh MJ, Zhou MM (2010) Molecular interplay of the noncoding RNA ANRIL and methylated histone H3 lysine 27 by polycomb CBX7 in transcriptional silencing of INK4a. Mol Cell 38(5):662–674
CAS
PubMed
PubMed Central
Article
Google Scholar
Yu M, Mazor T, Huang H, Huang HT, Kathrein KL, Woo AJ, Chouinard CR, Labadorf A, Akie TE, Moran TB, Xie H, Zacharek S, Taniuchi I, Roeder RG, Kim CF, Zon LI, Fraenkel E, Cantor AB (2012) Direct recruitment of polycomb repressive complex 1 to chromatin by core binding transcription factors. Mol Cell 45(3):330–343
CAS
PubMed
PubMed Central
Article
Google Scholar
Yuan W, Xu M, Huang C, Liu N, Chen S, Zhu B (2011) H3K36 methylation antagonizes PRC2-mediated H3K27 methylation. J Biol Chem 286(10):7983–7989
CAS
PubMed
PubMed Central
Article
Google Scholar
Yuan W, Wu T, Fu H, Dai C, Wu H, Liu N, Li X, Xu M, Zhang Z, Niu T, Han Z, Chai J, Zhou XJ, Gao S, Zhu B (2012) Dense chromatin activates Polycomb repressive complex 2 to regulate H3 lysine 27 methylation. Science 337(6097):971–975
CAS
PubMed
Article
Google Scholar
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 322(5902):750–756
CAS
PubMed
PubMed Central
Article
Google Scholar