Promiscuous RNA binding by Polycomb repressive complex 2 (original) (raw)

• Margueron, R. & Reinberg, D. The Polycomb complex PRC2 and its mark in life. Nature 469, 343–349 (2011).
  Article CAS Google Scholar
• Cao, R. & Zhang, Y. SUZ12 is required for both the histone methyltransferase activity and the silencing function of the EED-EZH2 complex. Mol. Cell 15, 57–67 (2004).
  Article CAS 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 Google Scholar
• Xu, C. et al. Binding of different histone marks differentially regulates the activity and specificity of polycomb repressive complex 2 (PRC2). Proc. Natl. Acad. Sci. USA 107, 19266–19271 (2010).
  Article CAS Google Scholar
• Yuan, W. et al. Dense chromatin activates Polycomb repressive complex 2 to regulate H3 lysine 27 methylation. Science 337, 971–975 (2012).
  Article CAS 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 Google Scholar
• Yuan, W. et al. H3K36 methylation antagonizes PRC2-mediated H3K27 methylation. J. Biol. Chem. 286, 7983–7989 (2011).
  Article CAS Google Scholar
• Boyer, L.A. et al. Polycomb complexes repress developmental regulators in murine embryonic stem cells. Nature 441, 349–353 (2006).
  Article CAS Google Scholar
• Lee, T.I. et al. Control of developmental regulators by Polycomb in human embryonic stem cells. Cell 125, 301–313 (2006).
  Article CAS Google Scholar
• Ram, O. et al. Combinatorial patterning of chromatin regulators uncovered by genome-wide location analysis in human cells. Cell 147, 1628–1639 (2011).
  Article CAS Google Scholar
• Bernstein, B.E. et al. A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell 125, 315–326 (2006).
  Article CAS Google Scholar
• Azuara, V. et al. Chromatin signatures of pluripotent cell lines. Nat. Cell Biol. 8, 532–538 (2006).
  Article CAS Google Scholar
• Roh, T.Y., Cuddapah, S., Cui, K. & Zhao, K. The genomic landscape of histone modifications in human T cells. Proc. Natl. Acad. Sci. USA 103, 15782–15787 (2006).
  Article CAS Google Scholar
• Mousavi, K., Zare, H., Wang, A.H. & Sartorelli, V. Polycomb protein Ezh1 promotes RNA polymerase II elongation. Mol. Cell 45, 255–262 (2012).
  Article CAS Google Scholar
• Herz, H.M. et al. Polycomb repressive complex 2-dependent and -independent functions of Jarid2 in transcriptional regulation in Drosophila. Mol. Cell. Biol. 32, 1683–1693 (2012).
  Article CAS Google Scholar
• Brookes, E. et al. Polycomb associates genome-wide with a specific RNA polymerase II variant, and regulates metabolic genes in ESCs. Cell Stem Cell 10, 157–170 (2012).
  Article CAS Google Scholar
• Ballaré, C. et al. Phf19 links methylated Lys36 of histone H3 to regulation of Polycomb activity. Nat. Struct. Mol. Biol. 19, 1257–1265 (2012).
  Article Google Scholar
• Musselman, C.A. et al. Molecular basis for H3K36me3 recognition by the Tudor domain of PHF1. Nat. Struct. Mol. Biol. 19, 1266–1272 (2012).
  Article CAS 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 Google Scholar
• Schwartz, Y.B. & Pirrotta, V. Polycomb silencing mechanisms and the management of genomic programmes. Nat. Rev. Genet. 8, 9–22 (2007).
  Article CAS Google Scholar
• Cuddapah, S. et al. A novel human polycomb binding site acts as a functional polycomb response element in Drosophila. PLoS ONE 7, e36365 (2012).
  Article CAS Google Scholar
• Sing, A. et al. A vertebrate Polycomb response element governs segmentation of the posterior hindbrain. Cell 138, 885–897 (2009).
  Article CAS Google Scholar
• Woo, C.J., Kharchenko, P.V., Daheron, L., Park, P.J. & Kingston, R.E. A region of the human HOXD cluster that confers polycomb-group responsiveness. Cell 140, 99–110 (2010).
  Article CAS Google Scholar
• Tsai, M.C. et al. Long noncoding RNA as modular scaffold of histone modification complexes. Science 329, 689–693 (2010).
  Article CAS Google Scholar
• Rinn, J.L. et al. Functional demarcation of active and silent chromatin domains in human s loci by noncoding RNAs. Cell 129, 1311–1323 (2007).
  Article CAS Google Scholar
• Chu, C., Qu, K., Zhong, F.L., Artandi, S.E. & Chang, H.Y. Genomic maps of long noncoding RNA occupancy reveal principles of RNA-chromatin interactions. Mol. Cell 44, 667–678 (2011).
  Article CAS 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 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 Google Scholar
• Zhao, J. et al. Genome-wide identification of polycomb-associated RNAs by RIP-seq. Mol. Cell 40, 939–953 (2010).
  Article CAS Google Scholar
• Khalil, A.M. 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 Google Scholar
• Guttman, M. et al. lincRNAs act in the circuitry controlling pluripotency and differentiation. Nature 477, 295–300 (2011).
  Article CAS Google Scholar
• Maenner, S. et al. 2-D structure of the A region of Xist RNA and its implication for PRC2 association. PLoS Biol. 8, e1000276 (2010).
  Article Google Scholar
• Duszczyk, M.M., Wutz, A., Rybin, V. & Sattler, M. The Xist RNA A-repeat comprises a novel AUCG tetraloop fold and a platform for multimerization. RNA 17, 1973–1982 (2011).
  Article CAS 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 Google Scholar
• Kowalczykowski, S.C. et al. Cooperative and noncooperative binding of protein ligands to nucleic acid lattices: experimental approaches to the determination of thermodynamic parameters. Biochemistry 25, 1226–1240 (1986).
  Article CAS Google Scholar
• Epstein, I.R. Kinetics of nucleic acid-large ligand interactions: exact Monte Carlo treatment and limiting cases of reversible binding. Biopolymers 18, 2037–2050 (1979).
  Article CAS Google Scholar
• Broderick, J.A., Salomon, W.E., Ryder, S.P., Aronin, N. & Zamore, P.D. Argonaute protein identity and pairing geometry determine cooperativity in mammalian RNA silencing. RNA 17, 1858–1869 (2011).
  Article CAS Google Scholar
• Record, M.T. Jr., Lohman, M.L. & De Haseth, P. Ion effects on ligand-nucleic acid interactions. J. Mol. Biol. 107, 145–158 (1976).
  Article CAS Google Scholar
• Makino, D.L., Baumgartner, M. & Conti, E. Crystal structure of an RNA-bound 11-subunit eukaryotic exosome complex. Nature 495, 70–75 (2013).
  Article CAS Google Scholar
• Mortazavi, A., Williams, B.A., McCue, K., Schaeffer, L. & Wold, B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat. Methods 5, 621–628 (2008).
  Article CAS Google Scholar
• Marks, H. et al. The transcriptional and epigenomic foundations of ground state pluripotency. Cell 149, 590–604 (2012).
  Article CAS Google Scholar
• Shaw, G., Morse, S., Ararat, M. & Graham, F.L. Preferential transformation of human neuronal cells by human adenoviruses and the origin of HEK 293 cells. FASEB J. 16, 869–871 (2002).
  Article CAS Google Scholar
• Schwartz, J.C. et al. FUS binds the CTD of RNA polymerase II and regulates its phosphorylation at Ser2. Genes Dev. 26, 2690–2695 (2012).
  Article CAS Google Scholar
• Ku, M. et al. Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains. PLoS Genet. 4, e1000242 (2008).
  Article Google Scholar
• Hansen, K.H. et al. A model for transmission of the H3K27me3 epigenetic mark. Nat. Cell Biol. 10, 1291–1300 (2008).
  Article CAS Google Scholar
• Sun, S. et al. Jpx RNA Activates Xist by evicting CTCF. Cell 153, 1537–1551 (2013).
  Article CAS Google Scholar
• Mazzone, J. & Pickett, J. The household diary study: mail use & attitudes in FY 2010. (US Postal Service 2011).
• Khersonsky, O. & Tawfik, D.S. Enzyme promiscuity: a mechanistic and evolutionary perspective. Annu. Rev. Biochem. 79, 471–505 (2010).
  Article CAS Google Scholar
• Murphy, F.L., Wang, Y.H., Griffith, J.D. & Cech, T.R. Coaxially stacked RNA helices in the catalytic center of the Tetrahymena ribozyme. Science 265, 1709–1712 (1994).
  Article CAS 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 Google Scholar
• Quinlan, A.R. & Hall, I.M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841–842 (2010).
  Article CAS Google Scholar
• Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).
  Article Google Scholar
• Robinson, J.T. et al. Integrative genomics viewer. Nat. Biotechnol. 29, 24–26 (2011).
  Article CAS Google Scholar
• Zhang, Y. et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 9, R137 (2008).
  Article Google Scholar
• Benjamini, Y. & Hochberg, Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. Ser. B 57, 289–300 (1995).
  Google Scholar
• Schwartz, J.C. et al. FUS binds the CTD of RNA polymerase II and regulates its phosphorylation at Ser2. Genes Dev. 26, 2690–2695 (2012).
  Article CAS Google Scholar
• Reimand, J., Kull, M., Peterson, H., Hansen, J. & Vilo, J. g:Profiler: a web-based toolset for functional profiling of gene lists from large-scale experiments. Nucleic Acids Res. 35, W193–W200 (2007).
  Article Google Scholar