The Mi-2 Homolog Mit1 Actively Positions Nucleosomes within Heterochromatin To Suppress Transcription

REFERENCES

• Elgin SC, Grewal SI. 2003. Heterochromatin: silence is golden. Curr. Biol. 13:R895–R898. http://dx.doi.org/10.1016/j.cub.2003.11.006.
   PubMed Web of Science ®Google Scholar
• Nakayama J, Rice JC, Strahl BD, Allis CD, Grewal SI. 2001. Role of histone H3 lysine 9 methylation in epigenetic control of heterochromatin assembly. Science 292:110–113. http://dx.doi.org/10.1126/science.1060118.
   PubMed Web of Science ®Google Scholar
• Rea S, Eisenhaber F, O'Carroll D, Strahl BD, Sun ZW, Schmid M, Opravil S, Mechtler K, Ponting CP, Allis CD, Jenuwein T. 2000. Regulation of chromatin structure by site-specific histone H3 methyltransferases. Nature 406:593–599. http://dx.doi.org/10.1038/35020506.
   PubMed Web of Science ®Google Scholar
• Bannister AJ, Zegerman P, Partridge JF, Miska EA, Thomas JO, Allshire RC, Kouzarides T. 2001. Selective recognition of methylated lysine 9 on histone H3 by the HP1 chromo domain. Nature 410:120–124. http://dx.doi.org/10.1038/35065138.
   PubMed Web of Science ®Google Scholar
• Sadaie M, Kawaguchi R, Ohtani Y, Arisaka F, Tanaka K, Shirahige K, Nakayama J. 2008. Balance between distinct HP1 family proteins controls heterochromatin assembly in fission yeast. Mol. Cell. Biol. 28:6973–6988. http://dx.doi.org/10.1128/MCB.00791-08.
   PubMedGoogle Scholar
• Motamedi MR, Hong EJ, Li X, Gerber S, Denison C, Gygi S, Moazed D. 2008. HP1 proteins form distinct complexes and mediate heterochromatic gene silencing by nonoverlapping mechanisms. Mol. Cell 32:778–790. http://dx.doi.org/10.1016/j.molcel.2008.10.026.
   PubMedGoogle Scholar
• Yamane K, Mizuguchi T, Cui B, Zofall M, Noma K, Grewal SI. 2011. Asf1/HIRA facilitate global histone deacetylation and associate with HP1 to promote nucleosome occupancy at heterochromatic loci. Mol. Cell 41:56–66. http://dx.doi.org/10.1016/j.molcel.2010.12.009.
   PubMedGoogle Scholar
• Fischer T, Cui B, Dhakshnamoorthy J, Zhou M, Rubin C, Zofall M, Veenstra TD, Grewal SI. 2009. Diverse roles of HP1 proteins in heterochromatin assembly and functions in fission yeast. Proc. Natl. Acad. Sci. U. S. A. 106:8998–9003. http://dx.doi.org/10.1073/pnas.0813063106.
   PubMed Web of Science ®Google Scholar
• Sugiyama T, Cam HP, Sugiyama R, Noma K, Zofall M, Kobayashi R, Grewal SI. 2007. SHREC, an effector complex for heterochromatic transcriptional silencing. Cell 128:491–504. http://dx.doi.org/10.1016/j.cell.2006.12.035.
   PubMed Web of Science ®Google Scholar
• Bjerling P, Silverstein RA, Thon G, Caudy A, Grewal S, Ekwall K. 2002. Functional divergence between histone deacetylases in fission yeast by distinct cellular localization and in vivo specificity. Mol. Cell. Biol. 22:2170–2181. http://dx.doi.org/10.1128/MCB.22.7.2170-2181.2002.
   PubMed Web of Science ®Google Scholar
• Bjerling P, Ekwall K, Egel R, Thon G. 2004. A novel type of silencing factor, Clr2, is necessary for transcriptional silencing at various chromosomal locations in the fission yeast Schizosaccharomyces pombe. Nucleic Acids Res. 32:4421–4428. http://dx.doi.org/10.1093/nar/gkh780.
   PubMedGoogle Scholar
• Thon G, Klar AJ. 1992. The clr1 locus regulates the expression of the cryptic mating-type loci of fission yeast. Genetics 131:287–296.
   PubMed Web of Science ®Google Scholar
• Thon G, Cohen A, Klar AJ. 1994. Three additional linkage groups that repress transcription and meiotic recombination in the mating-type region of Schizosaccharomyces pombe. Genetics 138:29–38.
   PubMedGoogle Scholar
• Ekwall K, Ruusala T. 1994. Mutations in rik1, clr2, clr3 and clr4 genes asymmetrically derepress the silent mating-type loci in fission yeast. Genetics 136:53–64.
   PubMed Web of Science ®Google Scholar
• Fazzio TG, Rando OJ. 2012. NURDs are required for diversity. EMBO J. 31:3036–3037. http://dx.doi.org/10.1038/emboj.2012.137.
   PubMedGoogle Scholar
• Sims JK, Wade PA. 2011. Mi-2/NuRD complex function is required for normal S phase progression and assembly of pericentric heterochromatin. Mol. Biol. Cell 22:3094–3102. http://dx.doi.org/10.1091/mbc.E11-03-0258.
   PubMedGoogle Scholar
• Pegoraro G, Kubben N, Wickert U, Gohler H, Hoffmann K, Misteli T. 2009. Ageing-related chromatin defects through loss of the NURD complex. Nat. Cell Biol. 11:1261–1267. http://dx.doi.org/10.1038/ncb1971.
   PubMed Web of Science ®Google Scholar
• Denslow SA, Wade PA. 2007. The human Mi-2/NuRD complex and gene regulation. Oncogene 26:5433–5438. http://dx.doi.org/10.1038/sj.onc.1210611.
   PubMed Web of Science ®Google Scholar
• Lantermann AB, Straub T, Stralfors A, Yuan GC, Ekwall K, Korber P. 2010. Schizosaccharomyces pombe genome-wide nucleosome mapping reveals positioning mechanisms distinct from those of Saccharomyces cerevisiae. Nat. Struct. Mol. Biol. 17:251–257. http://dx.doi.org/10.1038/nsmb.1741.
   PubMed Web of Science ®Google Scholar
• Garcia JF, Dumesic PA, Hartley PD, El-Samad H, Madhani HD. 2010. Combinatorial, site-specific requirement for heterochromatic silencing factors in the elimination of nucleosome-free regions. Genes Dev. 24:1758–1771. http://dx.doi.org/10.1101/gad.1946410.
   PubMed Web of Science ®Google Scholar
• Carvalho S, Raposo AC, Martins FB, Grosso AR, Sridhara SC, Rino J, Carmo-Fonseca M, de Almeida SF. 2013. Histone methyltransferase SETD2 coordinates FACT recruitment with nucleosome dynamics during transcription. Nucleic Acids Res. 41:2881–2893. http://dx.doi.org/10.1093/nar/gks1472.
   PubMed Web of Science ®Google Scholar
• Carrozza MJ, Li B, Florens L, Suganuma T, Swanson SK, Lee KK, Shia WJ, Anderson S, Yates J, Washburn MP, Workman JL. 2005. Histone H3 methylation by Set2 directs deacetylation of coding regions by Rpd3S to suppress spurious intragenic transcription. Cell 123:581–592. http://dx.doi.org/10.1016/j.cell.2005.10.023.
   PubMed Web of Science ®Google Scholar
• Petrie VJ, Wuitschick JD, Givens CD, Kosinski AM, Partridge JF. 2005. RNA interference (RNAi)-dependent and RNAi-independent association of the Chp1 chromodomain protein with distinct heterochromatic loci in fission yeast. Mol. Cell. Biol. 25:2331–2346. http://dx.doi.org/10.1128/MCB.25.6.2331-2346.2005.
   PubMed Web of Science ®Google Scholar
• Forsburg SL. 1993. Comparison of Schizosaccharomyces pombe expression systems. Nucleic Acids Res. 21:2955–2956. http://dx.doi.org/10.1093/nar/21.12.2955.
   PubMed Web of Science ®Google Scholar
• Guan KL, Dixon JE. 1991. Eukaryotic proteins expressed in Escherichia coli: an improved thrombin cleavage and purification procedure of fusion proteins with glutathione S-transferase. Anal. Biochem. 192:262–267. http://dx.doi.org/10.1016/0003-2697(91)90534-Z.
   PubMed Web of Science ®Google Scholar
• Punta M, Coggill PC, Eberhardt RY, Mistry J, Tate J, Boursnell C, Pang N, Forslund K, Ceric G, Clements J, Heger A, Holm L, Sonnhammer EL, Eddy SR, Bateman A, Finn RD. 2012. The Pfam protein families database. Nucleic Acids Res. 40:D290–D301. http://dx.doi.org/10.1093/nar/gkr1065.
   PubMed Web of Science ®Google Scholar
• Kelley LA, Sternberg MJ. 2009. Protein structure prediction on the Web: a case study using the Phyre server. Nat. Protoc. 4:363–371. http://dx.doi.org/10.1038/nprot.2009.2.
   PubMed Web of Science ®Google Scholar
• Leeds P, Peltz SW, Jacobson A, Culbertson MR. 1991. The product of the yeast UPF1 gene is required for rapid turnover of mRNAs containing a premature translational termination codon. Genes Dev. 5:2303–2314. http://dx.doi.org/10.1101/gad.5.12a.2303.
   PubMed Web of Science ®Google Scholar
• Hansen KR, Hazan I, Shanker S, Watt S, Verhein-Hansen J, Bahler J, Martienssen RA, Partridge JF, Cohen A, Thon G. 2011. H3K9me-independent gene silencing in fission yeast heterochromatin by Clr5 and histone deacetylases. PLoS Genet. 7:e1001268. http://dx.doi.org/10.1371/journal.pgen.1001268.
   PubMedGoogle Scholar
• Chang PY, Hom RA, Musselman CA, Zhu L, Kuo A, Gozani O, Kutateladze TG, Cleary ML. 2010. Binding of the MLL PHD3 finger to histone H3K4me3 is required for MLL-dependent gene transcription. J. Mol. Biol. 400:137–144. http://dx.doi.org/10.1016/j.jmb.2010.05.005.
   PubMed Web of Science ®Google Scholar
• Partridge JF, Debeauchamp JL, Kosinski AM, Ulrich DL, Hadler MJ, Noffsinger VJ. 2007. Functional separation of the requirements for establishment and maintenance of centromeric heterochromatin. Mol. Cell 26:593–602. http://dx.doi.org/10.1016/j.molcel.2007.05.004.
   PubMed Web of Science ®Google Scholar
• Moreno S, Klar A, Nurse P. 1991. Molecular genetic analysis of fission yeast Schizosaccharomyces pombe. Methods Enzymol. 194:795–823. http://dx.doi.org/10.1016/0076-6879(91)94059-L.
   PubMed Web of Science ®Google Scholar
• Sengupta SM, VanKanegan M, Persinger J, Logie C, Cairns BR, Peterson CL, Bartholomew B. 2001. The interactions of yeast SWI/SNF and RSC with the nucleosome before and after chromatin remodeling. J. Biol. Chem. 276:12636–12644.
   PubMedGoogle Scholar
• Shen X, Xiao H, Ranallo R, Wu WH, Wu C. 2003. Modulation of ATP-dependent chromatin-remodeling complexes by inositol polyphosphates. Science 299:112–114. http://dx.doi.org/10.1126/science.1078068.
   PubMed Web of Science ®Google Scholar
• Lantermann A, Stralfors A, Fagerstrom-Billai F, Korber P, Ekwall K. 2009. Genome-wide mapping of nucleosome positions in Schizosaccharomyces pombe. Methods 48:218–225. http://dx.doi.org/10.1016/j.ymeth.2009.02.004.
   PubMedGoogle Scholar
• Lai AY, Wade PA. 2011. Cancer biology and NuRD: a multifaceted chromatin remodelling complex. Nat. Rev. Cancer 11:588–596. http://dx.doi.org/10.1038/nrc3091.
   PubMedGoogle Scholar
• Hu G, Wade PA. 2012. NuRD and pluripotency: a complex balancing act. Cell Stem Cell 10:497–503. http://dx.doi.org/10.1016/j.stem.2012.04.011.
   PubMedGoogle Scholar
• Pointner J, Persson J, Prasad P, Norman-Axelsson U, Stralfors A, Khorosjutina O, Krietenstein N, Svensson JP, Ekwall K, Korber P. 2012. CHD1 remodelers regulate nucleosome spacing in vitro and align nucleosomal arrays over gene coding regions in S. pombe. EMBO J. 31:4388–4403. http://dx.doi.org/10.1038/emboj.2012.289.
   PubMed Web of Science ®Google Scholar
• Yamada T, Fischle W, Sugiyama T, Allis CD, Grewal SI. 2005. The nucleation and maintenance of heterochromatin by a histone deacetylase in fission yeast. Mol. Cell 20:173–185. http://dx.doi.org/10.1016/j.molcel.2005.10.002.
   PubMedGoogle Scholar
• Marina DB, Shankar S, Natarajan P, Finn KJ, Madhani HD. 2013. A conserved ncRNA-binding protein recruits silencing factors to heterochromatin through an RNAi-independent mechanism. Genes Dev. 27:1851–1856. http://dx.doi.org/10.1101/gad.226019.113.
   PubMed Web of Science ®Google Scholar
• Buhler M, Haas W, Gygi SP, Moazed D. 2007. RNAi-dependent and -independent RNA turnover mechanisms contribute to heterochromatic gene silencing. Cell 129:707–721. http://dx.doi.org/10.1016/j.cell.2007.03.038.
   PubMed Web of Science ®Google Scholar
• Schalch T, Job G, Shanker S, Partridge JF, Joshua-Tor L. 2011. The Chp1-Tas3 core is a multifunctional platform critical for gene silencing by RITS. Nat. Struct. Mol. Biol. 18:1351–1357. http://dx.doi.org/10.1038/nsmb.2151.
   PubMedGoogle Scholar
• Volpe TA, Kidner C, Hall IM, Teng G, Grewal SI, Martienssen RA. 2002. Regulation of heterochromatic silencing and histone H3 lysine-9 methylation by RNAi. Science 297:1833–1837. http://dx.doi.org/10.1126/science.1074973.
   PubMed Web of Science ®Google Scholar
• Verdel A, Jia S, Gerber S, Sugiyama T, Gygi S, Grewal SI, Moazed D. 2004. RNAi-mediated targeting of heterochromatin by the RITS complex. Science 303:672–676. http://dx.doi.org/10.1126/science.1093686.
   PubMed Web of Science ®Google Scholar
• Mueller-Planitz F, Klinker H, Ludwigsen J, Becker PB. 2013. The ATPase domain of ISWI is an autonomous nucleosome remodeling machine. Nat. Struct. Mol. Biol. 20:82–89.
   PubMedGoogle Scholar
• Okuda M, Horikoshi M, Nishimura Y. 2007. Structural polymorphism of chromodomains in Chd1. J. Mol. Biol. 365:1047–1062. http://dx.doi.org/10.1016/j.jmb.2006.10.039.
   PubMed Web of Science ®Google Scholar
• Bienz M. 2006. The PHD finger, a nuclear protein-interaction domain. Trends Biochem. Sci. 31:35–40. http://dx.doi.org/10.1016/j.tibs.2005.11.001.
   PubMed Web of Science ®Google Scholar
• Eissenberg JC. 2012. Structural biology of the chromodomain: form and function. Gene 496:69–78. http://dx.doi.org/10.1016/j.gene.2012.01.003.
   PubMedGoogle Scholar
• Marfella CG, Imbalzano AN. 2007. The Chd family of chromatin remodelers. Mutat. Res. 618:30–40. http://dx.doi.org/10.1016/j.mrfmmm.2006.07.012.
   PubMed Web of Science ®Google Scholar
• Hall JA, Georgel PT. 2007. CHD proteins: a diverse family with strong ties. Biochem. Cell Biol. 85:463–476. http://dx.doi.org/10.1139/O07-063.
   PubMed Web of Science ®Google Scholar
• Shi X, Hong T, Walter KL, Ewalt M, Michishita E, Hung T, Carney D, Pena P, Lan F, Kaadige MR, Lacoste N, Cayrou C, Davrazou F, Saha A, Cairns BR, Ayer DE, Kutateladze TG, Shi Y, Cote J, Chua KF, Gozani O. 2006. ING2 PHD domain links histone H3 lysine 4 methylation to active gene repression. Nature 442:96–99. http://dx.doi.org/10.1038/nature04835.
   PubMed Web of Science ®Google Scholar
• Mansfield RE, Musselman CA, Kwan AH, Oliver SS, Garske AL, Davrazou F, Denu JM, Kutateladze TG, Mackay JP. 2011. Plant homeodomain (PHD) fingers of CHD4 are histone H3-binding modules with preference for unmodified H3K4 and methylated H3K9. J. Biol. Chem. 286:11779–11791. http://dx.doi.org/10.1074/jbc.M110.208207.
   PubMed Web of Science ®Google Scholar
• Musselman CA, Mansfield RE, Garske AL, Davrazou F, Kwan AH, Oliver SS, O'Leary H, Denu JM, Mackay JP, Kutateladze TG. 2009. Binding of the CHD4 PHD2 finger to histone H3 is modulated by covalent modifications. Biochem. J. 423:179–187. http://dx.doi.org/10.1042/BJ20090870.
   PubMed Web of Science ®Google Scholar
• Musselman CA, Ramirez J, Sims JK, Mansfield RE, Oliver SS, Denu JM, Mackay JP, Wade PA, Hagman J, Kutateladze TG. 2012. Bivalent recognition of nucleosomes by the tandem PHD fingers of the CHD4 ATPase is required for CHD4-mediated repression. Proc. Natl. Acad. Sci. U. S. A. 109:787–792. http://dx.doi.org/10.1073/pnas.1113655109.
   PubMedGoogle Scholar
• Hota SK, Bartholomew B. 2011. Diversity of operation in ATP-dependent chromatin remodelers. Biochim. Biophys. Acta 1809:476–487. http://dx.doi.org/10.1016/j.bbagrm.2011.05.007.
   PubMedGoogle Scholar
• Meersseman G, Pennings S, Bradbury EM. 1992. Mobile nucleosomes—a general behavior. EMBO J. 11:2951–2959.
   PubMed Web of Science ®Google Scholar
• Lowary PT, Widom J. 1998. New DNA sequence rules for high affinity binding to histone octamer and sequence-directed nucleosome positioning. J. Mol. Biol. 276:19–42. http://dx.doi.org/10.1006/jmbi.1997.1494.
   PubMed Web of Science ®Google Scholar
• Tsukiyama T, Palmer J, Landel CC, Shiloach J, Wu C. 1999. Characterization of the imitation switch subfamily of ATP-dependent chromatin-remodeling factors in Saccharomyces cerevisiae. Genes Dev. 13:686–697. http://dx.doi.org/10.1101/gad.13.6.686.
   PubMed Web of Science ®Google Scholar
• Peterson CL. 2000. ATP-dependent chromatin remodeling: going mobile. FEBS Lett. 476:68–72. http://dx.doi.org/10.1016/S0014-5793(00)01673-2.
   PubMedGoogle Scholar
• Gangaraju VK, Bartholomew B. 2007. Dependency of ISW1a chromatin remodeling on extranucleosomal DNA. Mol. Cell. Biol. 27:3217–3225. http://dx.doi.org/10.1128/MCB.01731-06.
   PubMedGoogle Scholar
• Kaplan N, Moore IK, Fondufe-Mittendorf Y, Gossett AJ, Tillo D, Field Y, LeProust EM, Hughes TR, Lieb JD, Widom J, Segal E. 2009. The DNA-encoded nucleosome organization of a eukaryotic genome. Nature 458:362–366. http://dx.doi.org/10.1038/nature07667.
   PubMed Web of Science ®Google Scholar
• Xi L, Fondufe-Mittendorf Y, Xia L, Flatow J, Widom J, Wang JP. 2010. Predicting nucleosome positioning using a duration Hidden Markov Model. BMC Bioinformatics 11:346. http://dx.doi.org/10.1186/1471-2105-11-346.
   PubMedGoogle Scholar
• Yuan GC, Liu YJ, Dion MF, Slack MD, Wu LF, Altschuler SJ, Rando OJ. 2005. Genome-scale identification of nucleosome positions in S. cerevisiae. Science 309:626–630. http://dx.doi.org/10.1126/science.1112178.
   PubMed Web of Science ®Google Scholar
• Noma K, Grewal SI. 2002. Histone H3 lysine 4 methylation is mediated by Set1 and promotes maintenance of active chromatin states in fission yeast. Proc. Natl. Acad. Sci. U. S. A. 99(Suppl. 4):16438–16445. http://dx.doi.org/10.1073/pnas.182436399.
   PubMedGoogle Scholar
• Chen ES, Zhang K, Nicolas E, Cam HP, Zofall M, Grewal SI. 2008. Cell cycle control of centromeric repeat transcription and heterochromatin assembly. Nature 451:734–737. http://dx.doi.org/10.1038/nature06561.
   PubMed Web of Science ®Google Scholar
• Morris SA, Shibata Y, Noma K, Tsukamoto Y, Warren E, Temple B, Grewal SI, Strahl BD. 2005. Histone H3 K36 methylation is associated with transcription elongation in Schizosaccharomyces pombe. Eukaryot. Cell 4:1446–1454. http://dx.doi.org/10.1128/EC.4.8.1446-1454.2005.
   PubMedGoogle Scholar
• Ekwall K, Nimmo ER, Javerzat JP, Borgstrom B, Egel R, Cranston G, Allshire R. 1996. Mutations in the fission yeast silencing factors clr4+ and rik1+ disrupt the localisation of the chromo domain protein Swi6p and impair centromere function. J. Cell Sci. 109(Part 11):2637–2648.
   PubMedGoogle Scholar
• Kuryan BG, Kim J, Tran NN, Lombardo SR, Venkatesh S, Workman JL, Carey M. 2012. Histone density is maintained during transcription mediated by the chromatin remodeler RSC and histone chaperone NAP1 in vitro. Proc. Natl. Acad. Sci. U. S. A. 109:1931–1936. http://dx.doi.org/10.1073/pnas.1109994109.
   PubMedGoogle Scholar
• Lorch Y, Griesenbeck J, Boeger H, Maier-Davis B, Kornberg RD. 2011. Selective removal of promoter nucleosomes by the RSC chromatin-remodeling complex. Nat. Struct. Mol. Biol. 18:881–885. http://dx.doi.org/10.1038/nsmb.2072.
   PubMedGoogle Scholar
• Wang Y, Kallgren SP, Reddy BD, Kuntz K, Lopez-Maury L, Thompson J, Watt S, Ma C, Hou H, Shi Y, Yates JRIII, Bahler J, O'Connell MJ, Jia S. 2012. Histone H3 lysine 14 acetylation is required for activation of a DNA damage checkpoint in fission yeast. J. Biol. Chem. 287:4386–4393. http://dx.doi.org/10.1074/jbc.M111.329417.
   PubMedGoogle Scholar
• Reddy BD, Wang Y, Niu L, Higuchi EC, Marguerat SB, Bahler J, Smith GR, Jia S. 2011. Elimination of a specific histone H3K14 acetyltransferase complex bypasses the RNAi pathway to regulate pericentric heterochromatin functions. Genes Dev. 25:214–219. http://dx.doi.org/10.1101/gad.1993611.
   PubMed Web of Science ®Google Scholar
• Bouazoune K, Mitterweger A, Langst G, Imhof A, Akhtar A, Becker PB, Brehm A. 2002. The dMi-2 chromodomains are DNA binding modules important for ATP-dependent nucleosome mobilization. EMBO J. 21:2430–2440. http://dx.doi.org/10.1093/emboj/21.10.2430.
   PubMed Web of Science ®Google Scholar
• Brehm A, Langst G, Kehle J, Clapier CR, Imhof A, Eberharter A, Muller J, Becker PB. 2000. dMi-2 and ISWI chromatin remodelling factors have distinct nucleosome binding and mobilization properties. EMBO J. 19:4332–4341. http://dx.doi.org/10.1093/emboj/19.16.4332.
   PubMed Web of Science ®Google Scholar
• Watson AA, Mahajan P, Mertens HD, Deery MJ, Zhang W, Pham P, Du X, Bartke T, Zhang W, Edlich C, Berridge G, Chen Y, Burgess-Brown NA, Kouzarides T, Wiechens N, Owen-Hughes T, Svergun DI, Gileadi O, Laue ED. 2012. The PHD and chromo domains regulate the ATPase activity of the human chromatin remodeler CHD4. J. Mol. Biol. 422:3–17. http://dx.doi.org/10.1016/j.jmb.2012.04.031.
   PubMed Web of Science ®Google Scholar
• Wang HB, Zhang Y. 2001. Mi2, an auto-antigen for dermatomyositis, is an ATP-dependent nucleosome remodeling factor. Nucleic Acids Res. 29:2517–2521. http://dx.doi.org/10.1093/nar/29.12.2517.
   PubMedGoogle Scholar
• Shim YS, Choi Y, Kang K, Cho K, Oh S, Lee J, Grewal SI, Lee D. 2012. Hrp3 controls nucleosome positioning to suppress non-coding transcription in eu- and heterochromatin. EMBO J. 31:4375–4387. http://dx.doi.org/10.1038/emboj.2012.267.
   PubMedGoogle Scholar
• Whitehouse I, Tsukiyama T. 2006. Antagonistic forces that position nucleosomes in vivo. Nat. Struct. Mol. Biol. 13:633–640. http://dx.doi.org/10.1038/nsmb1111.
   PubMed Web of Science ®Google Scholar
• Mavrich TN, Ioshikhes IP, Venters BJ, Jiang C, Tomsho LP, Qi J, Schuster SC, Albert I, Pugh BF. 2008. A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome. Genome Res. 18:1073–1083. http://dx.doi.org/10.1101/gr.078261.108.
   PubMed Web of Science ®Google Scholar
• Joshi AA, Struhl K. 2005. Eaf3 chromodomain interaction with methylated H3–K36 links histone deacetylation to Pol II elongation. Mol. Cell 20:971–978. http://dx.doi.org/10.1016/j.molcel.2005.11.021.
   PubMed Web of Science ®Google Scholar
• Keogh MC, Kurdistani SK, Morris SA, Ahn SH, Podolny V, Collins SR, Schuldiner M, Chin K, Punna T, Thompson NJ, Boone C, Emili A, Weissman JS, Hughes TR, Strahl BD, Grunstein M, Greenblatt JF, Buratowski S, Krogan NJ. 2005. Cotranscriptional set2 methylation of histone H3 lysine 36 recruits a repressive Rpd3 complex. Cell 123:593–605. http://dx.doi.org/10.1016/j.cell.2005.10.025.
   PubMed Web of Science ®Google Scholar
• Strahl BD, Grant PA, Briggs SD, Sun ZW, Bone JR, Caldwell JA, Mollah S, Cook RG, Shabanowitz J, Hunt DF, Allis CD. 2002. Set2 is a nucleosomal histone H3-selective methyltransferase that mediates transcriptional repression. Mol. Cell. Biol. 22:1298–1306. http://dx.doi.org/10.1128/MCB.22.5.1298-1306.2002.
   PubMed Web of Science ®Google Scholar
• Smolle M, Venkatesh S, Gogol MM, Li H, Zhang Y, Florens L, Washburn MP, Workman JL. 2012. Chromatin remodelers Isw1 and Chd1 maintain chromatin structure during transcription by preventing histone exchange. Nat. Struct. Mol. Biol. 19:884–892. http://dx.doi.org/10.1038/nsmb.2312.
   PubMed Web of Science ®Google Scholar
• Venkatesh S, Smolle M, Li H, Gogol MM, Saint M, Kumar S, Natarajan K, Workman JL. 2012. Set2 methylation of histone H3 lysine 36 suppresses histone exchange on transcribed genes. Nature 489:452–455. http://dx.doi.org/10.1038/nature11326.
   PubMed Web of Science ®Google Scholar
• Hennig BP, Bendrin K, Zhou Y, Fischer T. 2012. Chd1 chromatin remodelers maintain nucleosome organization and repress cryptic transcription. EMBO Rep. 13:997–1003. http://dx.doi.org/10.1038/embor.2012.146.
   PubMedGoogle Scholar
• Kiely CM, Marguerat S, Garcia JF, Madhani HD, Bahler J, Winston F. 2011. Spt6 is required for heterochromatic silencing in the fission yeast Schizosaccharomyces pombe. Mol. Cell. Biol. 31:4193–4204. http://dx.doi.org/10.1128/MCB.05568-11.
   PubMed Web of Science ®Google Scholar
• Alper BJ, Job G, Yadav RK, Shanker S, Lowe BR, Partridge JF. 2013. Sir2 is required for Clr4 to initiate centromeric heterochromatin assembly in fission yeast. EMBO J. 32:2321–2335. http://dx.doi.org/10.1038/emboj.2013.143.
   PubMedGoogle Scholar
• Kato H, Okazaki K, Iida T, Nakayama J, Murakami Y, Urano T. 2013. Spt6 prevents transcription-coupled loss of posttranslationally modified histone H3. Sci. Rep. 3:2186. http://dx.doi.org/10.1038/srep02186.
   PubMed Web of Science ®Google Scholar
• Aygun O, Mehta S, Grewal SI. 2013. HDAC-mediated suppression of histone turnover promotes epigenetic stability of heterochromatin. Nat. Struct. Mol. Biol. 20:547–554. http://dx.doi.org/10.1038/nsmb.2565.
   PubMed Web of Science ®Google Scholar
• van Vugt JJ, de Jager M, Murawska M, Brehm A, van Noort J, Logie C. 2009. Multiple aspects of ATP-dependent nucleosome translocation by RSC and Mi-2 are directed by the underlying DNA sequence. PLoS One 4:e6345. http://dx.doi.org/10.1371/journal.pone.0006345.
   PubMedGoogle Scholar
• Lorch Y, Maier-Davis B, Kornberg RD. 2006. Chromatin remodeling by nucleosome disassembly in vitro. Proc. Natl. Acad. Sci. U. S. A. 103:3090–3093. http://dx.doi.org/10.1073/pnas.0511050103.
   PubMed Web of Science ®Google Scholar
• Whitehouse I, Rando OJ, Delrow J, Tsukiyama T. 2007. Chromatin remodelling at promoters suppresses antisense transcription. Nature 450:1031–1035. http://dx.doi.org/10.1038/nature06391.
   PubMed Web of Science ®Google Scholar
• Hartley PD, Madhani HD. 2009. Mechanisms that specify promoter nucleosome location and identity. Cell 137:445–458. http://dx.doi.org/10.1016/j.cell.2009.02.043.
   PubMed Web of Science ®Google Scholar
• Guschin D, Wade PA, Kikyo N, Wolffe AP. 2000. ATP-dependent histone octamer mobilization and histone deacetylation mediated by the Mi-2 chromatin remodeling complex. Biochemistry 39:5238–5245. http://dx.doi.org/10.1021/bi000421t.
   PubMedGoogle Scholar
• Helbling Chadwick L, Chadwick BP, Jaye DL, Wade PA. 2009. The Mi-2/NuRD complex associates with pericentromeric heterochromatin during S phase in rapidly proliferating lymphoid cells. Chromosoma 118:445–457. http://dx.doi.org/10.1007/s00412-009-0207-7.
   PubMedGoogle Scholar
• Hayden KE. 2012. Human centromere genomics: now it's personal. Chromosome Res. 20:621–633. http://dx.doi.org/10.1007/s10577-012-9295-y.
   PubMedGoogle Scholar