- Bonasio, R., Tu, S. & Reinberg, D. Molecular signals of epigenetic states. Science 330, 612–616 (2010).
Article CAS PubMed PubMed Central Google Scholar
- Margueron, R. & Reinberg, D. The Polycomb complex PRC2 and its mark in life. Nature 469, 343–349 (2011).
Article CAS PubMed PubMed Central Google Scholar
- Ringrose, L. & Paro, R. Epigenetic regulation of cellular memory by the Polycomb and Trithorax group proteins. Annu. Rev. Genet. 38, 413–443 (2004).
Article CAS PubMed Google Scholar
- Cao, R. et al. Role of histone H3 lysine 27 methylation in Polycomb-group silencing. Science 298, 1039–1043 (2002).
Article CAS PubMed Google Scholar
- Czermin, B. et al. Drosophila enhancer of Zeste/ESC complexes have a histone H3 methyltransferase activity that marks chromosomal Polycomb sites. Cell 111, 185–196 (2002).
Article CAS PubMed Google Scholar
- Kuzmichev, A., Nishioka, K., Erdjument-Bromage, H., Tempst, P. & Reinberg, D. Histone methyltransferase activity associated with a human multiprotein complex containing the Enhancer of Zeste protein. Genes Dev. 16, 2893–2905 (2002).
Article CAS PubMed PubMed Central Google Scholar
- Müller, J. et al. Histone methyltransferase activity of a Drosophila Polycomb group repressor complex. Cell 111, 197–208 (2002).
Article PubMed Google Scholar
- Margueron, R. et al. Role of the polycomb protein EED in the propagation of repressive histone marks. Nature 461, 762–767 (2009).
Article CAS PubMed PubMed Central Google Scholar
- Lewis, P.W. et al. Inhibition of PRC2 activity by a gain-of-function H3 mutation found in pediatric glioblastoma. Science 340, 857–861 (2013).
Article CAS PubMed PubMed Central Google Scholar
- Ernst, T. et al. Inactivating mutations of the histone methyltransferase gene EZH2 in myeloid disorders. Nat. Genet. 42, 722–726 (2010).
Article CAS PubMed Google Scholar
- Nikoloski, G. et al. Somatic mutations of the histone methyltransferase gene EZH2 in myelodysplastic syndromes. Nat. Genet. 42, 665–667 (2010).
Article CAS PubMed Google Scholar
- Shih, A.H., Abdel-Wahab, O., Patel, J.P. & Levine, R.L. The role of mutations in epigenetic regulators in myeloid malignancies. Nat. Rev. Cancer 12, 599–612 (2012).
Article CAS PubMed Google Scholar
- Margueron, R. et al. Ezh1 and Ezh2 maintain repressive chromatin through different mechanisms. Mol. Cell 32, 503–518 (2008).
Article CAS PubMed PubMed Central Google Scholar
- Rinn, J.L. et al. Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell 129, 1311–1323 (2007).
Article CAS PubMed PubMed Central Google Scholar
- Zhao, J., Sun, B.K., Erwin, J.A., Song, J.-J. & Lee, J.T. Polycomb proteins targeted by a short repeat RNA to the mouse X chromosome. Science 322, 750–756 (2008).
Article CAS PubMed PubMed Central Google Scholar
- Pandey, R.R. et al. Kcnq1ot1 antisense noncoding RNA mediates lineage-specific transcriptional silencing through chromatin-level regulation. Mol. Cell 32, 232–246 (2008).
Article CAS PubMed Google Scholar
- Khalil, A. et al. Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc. Natl. Acad. Sci. USA. 106, 11667–11672 (2009).
Article CAS PubMed PubMed Central Google Scholar
- Zhao, J. et al. Genome-wide identification of polycomb-associated RNAs by RIP-seq. Mol. Cell 40, 939–953 (2010).
Article CAS PubMed PubMed Central Google Scholar
- Klattenhoff, C.A. et al. Braveheart, a long noncoding RNA required for cardiovascular lineage commitment. Cell 152, 570–583 (2013).
Article CAS PubMed PubMed Central Google Scholar
- Kanhere, A. et al. Short RNAs are transcribed from repressed polycomb target genes and interact with polycomb repressive complex-2. Mol. Cell 38, 675–688 (2010).
Article CAS PubMed PubMed Central Google Scholar
- Brockdorff, N. Noncoding RNA and Polycomb recruitment. RNA 19, 429–442 (2013).
Article CAS PubMed PubMed Central Google Scholar
- Li, G. et al. Jarid2 and PRC2, partners in regulating gene expression. Genes Dev. 24, 368–380 (2010).
Article PubMed PubMed Central Google Scholar
- Kaneko, S. et al. Phosphorylation of the PRC2 component Ezh2 is cell cycle-regulated and up-regulates its binding to ncRNA. Genes Dev. 24, 2615–2620 (2010).
Article CAS PubMed PubMed Central Google Scholar
- Ciferri, C. et al. Molecular architecture of human polycomb repressive complex 2. eLife 1, e00005 (2012).
Article PubMed PubMed Central Google Scholar
- Jensen, K.B. & Darnell, R.B. CLIP: crosslinking and immunoprecipitation of in vivo RNA targets of RNA-binding proteins. Methods Mol. Biol. 488, 85–98 (2008).
Article CAS PubMed PubMed Central Google Scholar
- Hafner, M. et al. Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP. Cell 141, 129–141 (2010).
Article CAS PubMed PubMed Central Google Scholar
- Corcoran, D.L. et al. PARalyzer: definition of RNA binding sites from PAR-CLIP short-read sequence data. Genome Biol. 12, R79 (2011).
Article CAS PubMed PubMed Central Google Scholar
- Guttman, M. et al. lincRNAs act in the circuitry controlling pluripotency and differentiation. Nature 477, 295–300 (2011).
Article CAS PubMed PubMed Central Google Scholar
- Guil, S. et al. Intronic RNAs mediate EZH2 regulation of epigenetic targets. Nat. Struct. Mol. Biol. 19, 664–670 (2012).
Article CAS PubMed Google Scholar
- Boyer, L.A. et al. Polycomb complexes repress developmental regulators in murine embryonic stem cells. Nature 441, 349–353 (2006).
Article CAS PubMed Google Scholar
- Marks, H. et al. The transcriptional and epigenomic foundations of ground state pluripotency. Cell 149, 590–604 (2012).
Article CAS PubMed PubMed Central Google Scholar
- Mikkelsen, T.S. et al. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 448, 553–560 (2007).
Article CAS PubMed PubMed Central Google Scholar
- Ringrose, L. & Paro, R. Epigenetic regulation of cellular memory by the Polycomb and Trithorax group proteins. Annu. Rev. Genet. 38, 413–443 (2004).
Article CAS PubMed Google Scholar
- Mendenhall, E.M. et al. GC-rich sequence elements recruit PRC2 in mammalian ES cells. PLoS Genet. 6, e1001244 (2010).
Article PubMed PubMed Central Google Scholar
- Brien, G.L. et al. Polycomb PHF19 binds H3K36me3 and recruits PRC2 and demethylase NO66 to embryonic stem cell genes during differentiation. Nat. Struct. Mol. Biol. 19, 1273–1281 (2012).
Article CAS PubMed Google Scholar
- Kim, H., Kang, K. & Kim, J. AEBP2 as a potential targeting protein for Polycomb Repression Complex PRC2. Nucleic Acids Res. 37, 2940–2950 (2009).
Article CAS PubMed PubMed Central Google Scholar
- Voigt, P. et al. Asymmetrically modified nucleosomes. Cell 151, 181–193 (2012).
Article CAS PubMed PubMed Central Google Scholar
- Schmitges, F.W. et al. Histone methylation by PRC2 is inhibited by active chromatin marks. Mol. Cell 42, 330–341 (2011).
Article CAS PubMed Google Scholar
- Struhl, G. & Akam, M. Altered distributions of Ultrabithorax transcripts in extra sex combs mutant embryos of Drosophila. EMBO J. 4, 3259–3264 (1985).
Article CAS PubMed PubMed Central Google Scholar
- Papp, B. & Müller, J. Histone trimethylation and the maintenance of transcriptional ON and OFF states by trxG and PcG proteins. Genes Dev. 20, 2041–2054 (2006).
Article CAS PubMed PubMed Central Google Scholar
- Schmitt, S., Prestel, M. & Paro, R. Intergenic transcription through a polycomb group response element counteracts silencing. Genes Dev. 19, 697–708 (2005).
Article CAS PubMed PubMed Central Google Scholar
- Davidovich, C., Zheng, L., Goodrich, K.J. & Cech, T.R. Nat. Struct. Mol. Biol., 10.1038/nsmb.2679 (29 September 2013).
- Lee, J.T. Lessons from X-chromosome inactivation: long ncRNA as guides and tethers to the epigenome. Genes Dev. 23, 1831–1842 (2009).
Article CAS PubMed PubMed Central Google Scholar
- Kaneko, S., Rozenblatt-Rosen, O., Meyerson, M. & Manley, J.L. The multifunctional protein p54nrb/PSF recruits the exonuclease XRN2 to facilitate pre-mRNA 3′ processing and transcription termination. Genes Dev. 21, 1779–1789 (2007).
Article CAS PubMed PubMed Central Google Scholar
- Gao, Z. et al. PCGF homologs, CBX proteins, and RYBP define functionally distinct prc1 family complexes. Mol. Cell 45, 344–356 (2012).
Article CAS PubMed PubMed Central Google Scholar
- Hafner, M. et al. PAR-CliP: a method to identify transcriptome-wide the binding sites of RNA binding proteins. J. Vis. Exp. 41, 2034 (2010).
Google Scholar
- Rabani, M. et al. Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells. Nat. Biotechnol. 29, 436–442 (2011).
CAS PubMed PubMed Central Google Scholar
- Dölken, L. et al. High-resolution gene expression profiling for simultaneous kinetic parameter analysis of RNA synthesis and decay. RNA 14, 1959–1972 (2008).
Article PubMed PubMed Central Google Scholar
- Parkhomchuk, D. et al. Transcriptome analysis by strand-specific sequencing of complementary DNA. Nucleic Acids Res. 37, e123 (2009).
Article PubMed PubMed Central Google Scholar
- Langmead, B., Trapnell, C., Pop, M. & Salzberg, S.L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009).
Article PubMed PubMed Central Google Scholar
- Heinz, S. et al. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol. Cell 38, 576–589 (2010).
Article CAS PubMed PubMed Central Google Scholar
- Zhang, Y. et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 9, R137 (2008).
Article PubMed PubMed Central Google Scholar
- Ross-Innes, C.S. et al. Differential oestrogen receptor binding is associated with clinical outcome in breast cancer. Nature 481, 389–393 (2012).
Article CAS PubMed PubMed Central Google Scholar
- Wang, L., Feng, Z., Wang, X. & Zhang, X. DEGseq: an R package for identifying differentially expressed genes from RNA-seq data. Bioinformatics 26, 136–138 (2010).
Article PubMed Google Scholar
- Huang, D., Sherman, B.T. & Lempicki, R.A. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc. 4, 44–57 (2009).
Article CAS Google Scholar