The great repression

References

• Hennig BP, Bendrin K, Zhou Y, Fischer T. Chd1 chromatin remodelers maintain nucleosome organization and repress cryptic transcription. EMBO Rep 2012; 13:997 - 1003; http://dx.doi.org/10.1038/embor.2012.146; PMID: 23032292
   PubMed Web of Science ®Google Scholar
• Rando OJ, Chang HY. Genome-wide views of chromatin structure. Annu Rev Biochem 2009; 78:245 - 71; http://dx.doi.org/10.1146/annurev.biochem.78.071107.134639; PMID: 19317649
   PubMed Web of Science ®Google Scholar
• Zofall M, Fischer T, Zhang K, Zhou M, Cui B, Veenstra TD, et al. Histone H2A.Z cooperates with RNAi and heterochromatin factors to suppress antisense RNAs. Nature 2009; 461:419 - 22; http://dx.doi.org/10.1038/nature08321; PMID: 19693008
   PubMed Web of Science ®Google Scholar
• Lenstra TL, Benschop JJ, Kim T, Schulze JM, Brabers NA, Margaritis T, et al. The specificity and topology of chromatin interaction pathways in yeast. Mol Cell 2011; 42:536 - 49; http://dx.doi.org/10.1016/j.molcel.2011.03.026; PMID: 21596317
   PubMed Web of Science ®Google Scholar
• Carrozza MJ, Li B, Florens L, Suganuma T, Swanson SK, Lee KK, et al. Histone H3 methylation by Set2 directs deacetylation of coding regions by Rpd3S to suppress spurious intragenic transcription. Cell 2005; 123:581 - 92; http://dx.doi.org/10.1016/j.cell.2005.10.023; PMID: 16286007
   PubMed Web of Science ®Google Scholar
• Gkikopoulos T, Schofield P, Singh V, Pinskaya M, Mellor J, Smolle M, et al. A role for Snf2-related nucleosome-spacing enzymes in genome-wide nucleosome organization. Science 2011; 333:1758 - 60; http://dx.doi.org/10.1126/science.1206097; PMID: 21940898
   PubMed Web of Science ®Google Scholar
• Smolle M, Venkatesh S, Gogol MM, Li H, Zhang Y, Florens L, et al. Chromatin remodelers Isw1 and Chd1 maintain chromatin structure during transcription by preventing histone exchange. Nat Struct Mol Biol 2012; 19:884 - 92; http://dx.doi.org/10.1038/nsmb.2312; PMID: 22922743
   PubMed Web of Science ®Google Scholar
• Shim YS, Choi Y, Kang K, Cho K, Oh S, Lee J, et al. Hrp3 controls nucleosome positioning to suppress non-coding transcription in eu- and heterochromatin. EMBO J 2012; 31:4375 - 87; http://dx.doi.org/10.1038/emboj.2012.267; PMID: 22990236
   PubMed Web of Science ®Google Scholar
• Sekinger EA, Moqtaderi Z, Struhl K. Intrinsic histone-DNA interactions and low nucleosome density are important for preferential accessibility of promoter regions in yeast. Mol Cell 2005; 18:735 - 48; http://dx.doi.org/10.1016/j.molcel.2005.05.003; PMID: 15949447
   PubMed Web of Science ®Google Scholar
• Cheung V, Chua G, Batada NN, Landry CR, Michnick SW, Hughes TR, et al. Chromatin- and transcription-related factors repress transcription from within coding regions throughout the Saccharomyces cerevisiae genome. PLoS Biol 2008; 6:e277; http://dx.doi.org/10.1371/journal.pbio.0060277; PMID: 18998772
   PubMed Web of Science ®Google Scholar
• Silva AC, Xu X, Kim HS, Fillingham J, Kislinger T, Mennella TA, et al. The replication-independent histone H3-H4 chaperones HIR, ASF1, and RTT106 co-operate to maintain promoter fidelity. J Biol Chem 2012; 287:1709 - 18; http://dx.doi.org/10.1074/jbc.M111.316489; PMID: 22128187
   PubMed Web of Science ®Google Scholar
• Pattenden SG, Gogol MM, Workman JL. Features of cryptic promoters and their varied reliance on bromodomain-containing factors. PLoS One 2010; 5:e12927; http://dx.doi.org/10.1371/journal.pone.0012927; PMID: 20886085
   PubMedGoogle Scholar
• Gunjan A, Paik J, Verreault A. The emergence of regulated histone proteolysis. Curr Opin Genet Dev 2006; 16:112 - 8; http://dx.doi.org/10.1016/j.gde.2006.02.010; PMID: 16510276
   PubMed Web of Science ®Google Scholar
• Feser J, Truong D, Das C, Carson JJ, Kieft J, Harkness T, et al. Elevated histone expression promotes life span extension. Mol Cell 2010; 39:724 - 35; http://dx.doi.org/10.1016/j.molcel.2010.08.015; PMID: 20832724
   PubMed Web of Science ®Google Scholar
• Formosa T, Ruone S, Adams MD, Olsen AE, Eriksson P, Yu Y, et al. Defects in SPT16 or POB3 (yFACT) in Saccharomyces cerevisiae cause dependence on the Hir/Hpc pathway: polymerase passage may degrade chromatin structure. Genetics 2002; 162:1557 - 71; PMID: 12524332
   PubMed Web of Science ®Google Scholar
• Belotserkovskaya R, Oh S, Bondarenko VA, Orphanides G, Studitsky VM, Reinberg D. FACT facilitates transcription-dependent nucleosome alteration. Science 2003; 301:1090 - 3; http://dx.doi.org/10.1126/science.1085703; PMID: 12934006
   PubMed Web of Science ®Google Scholar
• Formosa T. FACT and the reorganized nucleosome. Mol Biosyst 2008; 4:1085 - 93; http://dx.doi.org/10.1039/b812136b; PMID: 18931784
   PubMed Web of Science ®Google Scholar
• Kaplan CD, Laprade L, Winston F. Transcription elongation factors repress transcription initiation from cryptic sites. Science 2003; 301:1096 - 9; http://dx.doi.org/10.1126/science.1087374; PMID: 12934008
   PubMed Web of Science ®Google Scholar
• Mason PB, Struhl K. The FACT complex travels with elongating RNA polymerase II and is important for the fidelity of transcriptional initiation in vivo. Mol Cell Biol 2003; 23:8323 - 33; http://dx.doi.org/10.1128/MCB.23.22.8323-8333.2003; PMID: 14585989
   PubMed Web of Science ®Google Scholar
• Celona B, Weiner A, Di Felice F, Mancuso FM, Cesarini E, Rossi RL, et al. Substantial histone reduction modulates genomewide nucleosomal occupancy and global transcriptional output. PLoS Biol 2011; 9:e1001086; http://dx.doi.org/10.1371/journal.pbio.1001086; PMID: 21738444
   PubMed Web of Science ®Google Scholar
• Quan TK, Hartzog GA. Histone H3K4 and K36 methylation, Chd1 and Rpd3S oppose the functions of Saccharomyces cerevisiae Spt4-Spt5 in transcription. Genetics 2010; 184:321 - 34; http://dx.doi.org/10.1534/genetics.109.111526; PMID: 19948887
   PubMed Web of Science ®Google Scholar
• Pointner J, Persson J, Prasad P, Norman-Axelsson U, Strålfors A, Khorosjutina O, et al. CHD1 remodelers regulate nucleosome spacing in vitro and align nucleosomal arrays over gene coding regions in S. pombe. EMBO J 2012; 31:4388 - 403; http://dx.doi.org/10.1038/emboj.2012.289; PMID: 23103765
   PubMed Web of Science ®Google Scholar
• Keogh MC, Kurdistani SK, Morris SA, Ahn SH, Podolny V, Collins SR, et al. Cotranscriptional set2 methylation of histone H3 lysine 36 recruits a repressive Rpd3 complex. Cell 2005; 123:593 - 605; http://dx.doi.org/10.1016/j.cell.2005.10.025; PMID: 16286008
   PubMed Web of Science ®Google Scholar
• Nakayama J, Xiao G, Noma K, Malikzay A, Bjerling P, Ekwall K, et al. Alp13, an MRG family protein, is a component of fission yeast Clr6 histone deacetylase required for genomic integrity. EMBO J 2003; 22:2776 - 87; http://dx.doi.org/10.1093/emboj/cdg248; PMID: 12773392
   PubMed Web of Science ®Google Scholar
• Nicolas E, Yamada T, Cam HP, Fitzgerald PC, Kobayashi R, Grewal SI. Distinct roles of HDAC complexes in promoter silencing, antisense suppression and DNA damage protection. Nat Struct Mol Biol 2007; 14:372 - 80; http://dx.doi.org/10.1038/nsmb1239; PMID: 17450151
   PubMed Web of Science ®Google Scholar
• Kim T, Xu Z, Clauder-Münster S, Steinmetz LM, Buratowski S. Set3 HDAC mediates effects of overlapping noncoding transcription on gene induction kinetics. Cell 2012; 150:1158 - 69; http://dx.doi.org/10.1016/j.cell.2012.08.016; PMID: 22959268
   PubMed Web of Science ®Google Scholar
• Krogan NJ, Kim M, Tong A, Golshani A, Cagney G, Canadien V, et al. Methylation of histone H3 by Set2 in Saccharomyces cerevisiae is linked to transcriptional elongation by RNA polymerase II. Mol Cell Biol 2003; 23:4207 - 18; http://dx.doi.org/10.1128/MCB.23.12.4207-4218.2003; PMID: 12773564
   PubMed Web of Science ®Google Scholar
• Xiao T, Hall H, Kizer KO, Shibata Y, Hall MC, Borchers CH, et al. Phosphorylation of RNA polymerase II CTD regulates H3 methylation in yeast. Genes Dev 2003; 17:654 - 63; http://dx.doi.org/10.1101/gad.1055503; PMID: 12629047
   PubMed Web of Science ®Google Scholar
• Govind CK, Qiu H, Ginsburg DS, Ruan C, Hofmeyer K, Hu C, et al. Phosphorylated Pol II CTD recruits multiple HDACs, including Rpd3C(S), for methylation-dependent deacetylation of ORF nucleosomes. Mol Cell 2010; 39:234 - 46; http://dx.doi.org/10.1016/j.molcel.2010.07.003; PMID: 20670892
   PubMed Web of Science ®Google Scholar
• Drouin S, Laramée L, Jacques PÉ, Forest A, Bergeron M, Robert F. DSIF and RNA polymerase II CTD phosphorylation coordinate the recruitment of Rpd3S to actively transcribed genes. PLoS Genet 2010; 6:e1001173; http://dx.doi.org/10.1371/journal.pgen.1001173; PMID: 21060864
   PubMed Web of Science ®Google Scholar
• Venkatesh S, Smolle M, Li H, Gogol MM, Saint M, Kumar S, et al. Set2 methylation of histone H3 lysine 36 suppresses histone exchange on transcribed genes. Nature 2012; 489:452 - 5; http://dx.doi.org/10.1038/nature11326; PMID: 22914091
   PubMed Web of Science ®Google Scholar
• Radman-Livaja M, Quan TK, Valenzuela L, Armstrong JA, van Welsem T, Kim T, et al. A key role for Chd1 in histone H3 dynamics at the 3′ ends of long genes in yeast. PLoS Genet 2012; 8:e1002811; http://dx.doi.org/10.1371/journal.pgen.1002811; PMID: 22807688
   PubMedGoogle Scholar
• Lee JS, Garrett AS, Yen K, Takahashi YH, Hu D, Jackson J, et al. Codependency of H2B monoubiquitination and nucleosome reassembly on Chd1. Genes Dev 2012; 26:914 - 9; http://dx.doi.org/10.1101/gad.186841.112; PMID: 22549955
   PubMed Web of Science ®Google Scholar
• Zentner GE, Tsukiyama T, Henikoff S. ISWI and CHD chromatin remodelers bind promoters but act in gene bodies. PLoS Genet 2013; 9:e1003317; http://dx.doi.org/10.1371/journal.pgen.1003317; PMID: 23468649
   PubMed Web of Science ®Google Scholar
• Smolle M, Workman JL, Venkatesh S. reSETting chromatin during transcription elongation. Epigenetics 2012; 8:10 - 5; http://dx.doi.org/10.4161/epi.23333; PMID: 23257840
   PubMed Web of Science ®Google Scholar
• Raisner RM, Hartley PD, Meneghini MD, Bao MZ, Liu CL, Schreiber SL, et al. Histone variant H2A.Z marks the 5′ ends of both active and inactive genes in euchromatin. Cell 2005; 123:233 - 48; http://dx.doi.org/10.1016/j.cell.2005.10.002; PMID: 16239142
   PubMed Web of Science ®Google Scholar
• Venters BJ, Pugh BF. A canonical promoter organization of the transcription machinery and its regulators in the Saccharomyces genome. Genome Res 2009; 19:360 - 71; http://dx.doi.org/10.1101/gr.084970.108; PMID: 19124666
   PubMed Web of Science ®Google Scholar
• Raveh-Sadka T, Levo M, Shabi U, Shany B, Keren L, Lotan-Pompan M, et al. Manipulating nucleosome disfavoring sequences allows fine-tune regulation of gene expression in yeast. Nat Genet 2012; 44:743 - 50; http://dx.doi.org/10.1038/ng.2305; PMID: 22634752
   PubMed Web of Science ®Google Scholar
• Gossett AJ, Lieb JD. In vivo effects of histone H3 depletion on nucleosome occupancy and position in Saccharomyces cerevisiae. PLoS Genet 2012; 8:e1002771; http://dx.doi.org/10.1371/journal.pgen.1002771; PMID: 22737086
   PubMed Web of Science ®Google Scholar
• Hartley PD, Madhani HD. Mechanisms that specify promoter nucleosome location and identity. Cell 2009; 137:445 - 58; http://dx.doi.org/10.1016/j.cell.2009.02.043; PMID: 19410542
   PubMed Web of Science ®Google Scholar