Silent chromatin at the middle and ends: Lessons from yeasts

EMBO Journal

Volumn 28, Issue 15, 2009, Pages 2149-2161

  Bühler, Marc ^a   Gasser, Susan M ^a  

^a FRIEDRICH MIESCHER INSTITUTE FOR BIOMEDICAL RESEARCH   (Switzerland)

Author keywords

Heterochromatin; RNA; Silencing

Indexed keywords

CENTROMERE; CHROMATIN; CHROMATIN STRUCTURE; DNA SEQUENCE; EPIGENETICS; HETEROCHROMATIN; NONHUMAN; PRIORITY JOURNAL; REVIEW; SACCHAROMYCES CEREVISIAE; SCHIZOSACCHAROMYCES POMBE; SILENT CHROMATIN; TELOMERE;

CENTROMERE; CHROMOSOMES; HETEROCHROMATIN; MODELS, BIOLOGICAL; SACCHAROMYCES CEREVISIAE; SCHIZOSACCHAROMYCES; TELOMERE;

EUKARYOTA; SACCHAROMYCES CEREVISIAE; SCHIZOSACCHAROMYCES POMBE; SCHIZOSACCHAROMYCETACEAE;

EID: 68249153738     PISSN: 02614189     EISSN: 14602075     Source Type: Journal    
DOI: 10.1038/emboj.2009.185     Document Type: Review

References (150)

1. Akhtar A, Gasser SM (2007) The nuclear envelope and transcriptional control. Nat Rev Genet 8: 507-517
2. Alfredsson-Timmins J, Henningson F, Bjerling P (2007) The Clr4 methyltransferase determines the subnuclear localization of the mating-type region in fission yeast. J Cell Sci 120 (Pt 11): 1935-1943
3. Allshire RC, Javerzat JP, Redhead NJ, Cranston G (1994) Position effect variegation at fission yeast centromeres. Cell 76: 157-169
4. Allshire RC, Karpen GH (2008) Epigenetic regulation of centromeric chromatin: old dogs, new tricks? Nat Rev Genet 9: 923-937
5. Allshire RC, Nimmo ER, Ekwall K, Javerzat JP, Cranston G (1995) Mutations derepressing silent centromeric domains in fission yeast disrupt chromosome segregation. Genes Dev 9: 218-233
6. Andrulis ED, Neiman AM, Zappulla DC, Sternglanz R (1998) Perinuclear localization of chromatin facilitates transcriptional silencing. Nature 394: 592-595
7. Antoniacci LM, Kenna MA, Skibbens RV (2007) The nuclear envelope and spindle pole body-associated Mps3 protein bind telomere regulators and function in telomere clustering. Cell Cycle 6: 75-79
8. Aparicio OM, Billington BL, Gottschling DE (1991) Modifiers of position effect are shared between telomeric and silent mating-type loci in S. cerevisiae. Cell 66: 1279-1287
9. Ayoub N, Goldshmidt I, Lyakhovetsky R, Cohen A (2000) A fission yeast repression element cooperates with centromere-like sequences and defines a mat silent domain boundary. Genetics 156: 983-994
10. Azzalin CM, Reichenbach P, Khoriauli L, Giulotto E, Lingner J (2007) Telomeric repeat containing RNA and RNA surveillance factors at mammalian chromosome ends. Science 318: 798-801
11. Bartel DP (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116: 281-297
12. Bernstein E, Allis CD (2005) RNA meets chromatin. Genes Dev 19: 1635-1655
13. Bernstein E, Caudy AA, Hammond SM, Hannon GJ (2001) Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature 409: 363-366
14. Berretta J, Pinskaya M, Morillon A (2008) A cryptic unstable transcript mediates transcriptional trans-silencing of the Ty1 retrotransposon in S cerevisiae. Genes Dev 22: 615-626
15. Bjerling P, Ekwall K (2002) Centromere domain organization and histone modifications. Braz J Med Biol Res 35: 499-507
16. 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
17. Blander G, Guarente L (2004) The Sir2 family of protein deacetylases. Annu Rev Biochem 73: 417-435
18. Braunstein M, Sobel RE, Allis CD, Turner BM, Broach JR (1996) Efficient transcriptional silencing in Saccharomyces cerevisiae requires a heterochromatin histone acetylation pattern. Mol Cell Biol 16: 4349-4356
19. Buck SW, Shore D (1995) Action of a RAP1 carboxy-terminal silencing domain reveals an underlying competition between HMR and telomeres in yeast. Genes Dev 9: 370-384
20. Buhler M (2009) RNA turnover and chromatin-dependent gene silencing. Chromosoma 118: 141-151
21. 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
22. Buhler M, Moazed D (2007) Transcription and RNAi in heterochromatic gene silencing. Nat Struct Mol Biol 14: 1041-1048
23. Buhler M, Spies N, Bartel DP, Moazed D (2008) TRAMP-mediated RNA surveillance prevents spurious entry of RNAs into the Schizosaccharomyces pombe siRNA pathway. Nat Struct Mol Biol 15: 1015-1023
24. Buhler M, Verdel A, Moazed D (2006) Tethering RITS to a nascent transcript initiates RNAi- and heterochromatin-dependent gene silencing. Cell 125: 873-886
25. Buker SM, Iida T, Buhler M, Villen J, Gygi SP, Nakayama J, Moazed D (2007) Two different Argonaute complexes are required for siRNA generation and heterochromatin assembly in fission yeast. Nat Struct Mol Biol 14: 200-207
26. Bupp J, Martin A, Stensrud E, Jaspersen S (2007) Telomere anchoring at the nuclear periphery requires the budding yeast Sad1-UNC-84 domain protein Mps3. J Cell Biol 179: 845-854
27. Cam HP, Chen ES, Grewal SI (2009) Transcriptional scaffolds for heterochromatin assembly. Cell 136: 610-614
28. Cam HP, Sugiyama T, Chen ES, Chen X, FitzGerald PC, Grewal SI (2005) Comprehensive analysis of heterochromatin- and RNAi-mediated epigenetic control of the fission yeast genome. Nat Genet 37: 809-819
29. Camblong J, Iglesias N, Fickentscher C, Dieppois G, Stutz F (2007) Antisense RNA stabilization induces transcriptional gene silencing via histone deacetylation in S Cerevisiae. Cell 131: 706-717
30. Caudy AA, Ketting RF, Hammond SM, Denli AM, Bathoorn AM, Tops BB, Silva JM, Myers MM, Hannon GJ, Plasterk RH (2003) A micrococcal nuclease homologue in RNAi effector complexes. Nature 425: 411-414
31. Caudy AA, Myers M, Hannon GJ, Hammond SM (2002) Fragile X-related protein and VIG associate with the RNA interference machinery. Genes Dev 16: 2491-2496
32. Cheng TH, Li YC, Gartenberg MR (1998) Persistence of an alternate chromatin structure at silenced loci in the absence of silencers. Proc Natl Acad Sci USA 95: 5521-5526
33. Chikashige Y, Ding DQ, Imai Y, Yamamoto M, Haraguchi T, Hiraoka Y (1997) Meiotic nuclear reorganization: switching the position of centromeres and telomeres in the fission yeast Schizosaccharomyces pombe. EMBO J 16: 193-202
34. Chou CC, Li YC, Gartenberg MR (2008) Bypassing Sir2 and O-acetyl-ADP-ribose in transcriptional silencing. Mol Cell 31: 650-659
35. Cockell M, Gotta M, Palladino F, Martin SG, Gasser SM (1998) Targeting Sir proteins to sites of action: a general mechanism for regulated repression. Cold Spring Harb Symp Quant Biol 63: 401-412
36. Cooper JP, Watanabe Y, Nurse P (1998) Fission yeast Taz1 protein is required for meiotic telomere clustering and recombination. Nature 392: 828-831
37. Cubizolles F, Martino F, Perrod S, Gasser SM (2006) A homotrimer-heterotrimer switch in Sir2 structure differentiates rDNA and telomeric silencing. Mol Cell 21: 825-836
38. Dalmay T, Hamilton A, Rudd S, Angell S, Baulcombe DC (2000) An RNA-dependent RNA polymerase gene in Arabidopsis is required for posttranscriptional gene silencing mediated by a transgene but not by a virus. Cell 101: 543-553
39. de Laat W, Grosveld F (2007) Inter-chromosomal gene regulation in the mammalian cell nucleus. Curr Opin Genet Dev 17: 456-464
40. Djupedal I, Portoso M, Spahr H, Bonilla C, Gustafsson CM, Allshire RC, Ekwall K (2005) RNA Pol II subunit Rpb7 promotes centromeric transcription and RNAi-directed chromatin silencing. Genes Dev 19: 2301-2306
41. 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(Pt 11): 2637-2648
42. Fisher TS, Zakian VA (2005) Ku: a multifunctional protein involved in telomere maintenance. DNA Repair (Amst) 4: 1215-1226
43. Folco HD, Pidoux AL, Urano T, Allshire RC (2008) Heterochromatin and RNAi are required to establish CENP-A chromatin at centromeres. Science 319: 94-97
44. Fridkin A, Penkner A, Jantsch V, Gruenbaum Y (2008) SUN-domain and KASH-domain proteins during development, meiosis and disease. Cell Mol Life Sci (E-pub ahead of print)
45. Funabiki H, Hagan I, Uzawa S, Yanagida M (1993) Cell cycle-dependent specific positioning and clustering of centromeres and telomeres in fission yeast. J Cell Biol 121: 961-976
46. Furuyama S, Biggins S (2007) Centromere identity is specified by a single centromeric nucleosome in budding yeast. Proc Natl Acad Sci USA 104: 14706-14711
47. Gao L, Gross DS (2008) Sir2 silences gene transcription by targeting the transition between RNA polymerase II initiation and elongation. Mol Cell Biol 28: 3979-3994
48. Gartenberg MR (2009) Life on the edge: telomeres and persistent DNA breaks converge at the nuclear periphery. Genes Dev 23: 1027-1031
49. Gartenberg MR, Neumann FR, Laroche T, Blaszczyk M, Gasser SM (2004) Sir-mediated repression can occur independently of chromosomal and subnuclear contexts. Cell 119: 955-967
50. Gottschling DE (1992) Telomere-proximal DNA in Saccharomyces cerevisiae is refractory to methyltransferase activity in vivo. Proc Natl Acad Sci USA 89: 4062-4065
51. Gottschling DE, Aparicio OM, Billington BL, Zakian VA (1990) Position effect at S. cerevisiae telomeres: reversible repression of Pol II transcription. Cell 63: 751-762
52. Gravel S, Larrivee M, Labrecque P, Wellinger RJ (1998) Yeast Ku as a regulator of chromosomal DNA end structure. Science 280: 741-744
53. Grewal SI, Bonaduce MJ, Klar AJ (1998) Histone deacetylase homologs regulate epigenetic inheritance of transcriptional silencing and chromosome segregation in fission yeast. Genetics 150: 563-576
54. Grewal SI, Elgin SC (2007) Transcription and RNA interference in the formation of heterochromatin. Nature 447: 399-406
55. Grewal SI, Moazed D (2003) Heterochromatin and epigenetic control of gene expression. Science 301: 798-802
56. Hall IM, Noma K, Grewal SI (2003) RNA interference machinery regulates chromosome dynamics during mitosis and meiosis in fission yeast. Proc Natl Acad Sci USA 100: 193-198
57. Hammond SM, Boettcher S, Caudy AA, Kobayashi R, Hannon GJ (2001) Argonaute2, a link between genetic and biochemical analyses of RNAi. Science 293: 1146-1150
58. Hannon GJ (2002) RNA interference. Nature 418: 244-251
59. Hecht A, Laroche T, Strahl-Bolsinger S, Gasser SM, Grunstein M (1995) Histone H3 and H4 N-termini interact with SIR3 and SIR4 proteins: a molecular model for the formation of heterochromatin in yeast. Cell 80: 583-592
60. Hecht A, Strahl-Bolsinger S, Grunstein M (1996) Spreading of transcriptional repressor SIR3 from telomeric heterochromatin. Nature 383: 92-96
61. Hediger F, Neumann FR, Van Houwe G, Dubrana K, Gasser SM (2002) Live Imaging of telomeres. yKu and Sir proteins define redundant telomere-anchoring pathways in yeast. Curr Biol 12: 2076-2089
62. Hirota K, Miyoshi T, Kugou K, Hoffman CS, Shibata T, Ohta K (2008) Stepwise chromatin remodelling by a cascade of transcription initiation of non-coding RNAs. Nature 456: 130-134
63. Holmes SG, Broach JR (1996) Silencers are required for inheritance of the repressed state in yeast. Genes Dev 10: 1021-1032
64. Hongay CF, Grisafi PL, Galitski T, Fink GR (2006) Antisense transcription controls cell fate in Saccharomyces cerevisiae. Cell 127: 735-745
65. Houseley J, Kotovic K, El Hage A, Tollervey D (2007) Trf4 targets ncRNAs from telomeric and rDNA spacer regions and functions in rDNA copy number control. EMBO J 26: 4996-5006
66. Huang Y (2002) Transcriptional silencing in Saccharomyces cerevisiae and Schizosaccharomyces pombe. Nucleic Acids Res 30: 1465-1482
67. Hutvagner G, Zamore PD (2002) A microRNA in a multiple-turnover RNAi enzyme complex. Science 297: 2056-2060
68. Imai S, Armstrong CM, Kaeberlein M, Guarente L (2000) Transcriptional silencing and longevity protein Sir2 is an NAD-dependent histone deacetylase. Nature 403: 795-800
69. Irvine DV, Zaratiegui M, Tolia NH, Goto DB, Chitwood DH, Vaughn MW, Joshua-Tor L, Martienssen RA (2006) Argonaute slicing is required for heterochromatic silencing and spreading. Science 313: 1134-1137
70. Jacobs SA, Khorasanizadeh S (2002) Structure of HP1 chromodomain bound to a lysine 9-methylated histone H3 tail. Science 295: 2080-2083
71. Jacobs SA, Taverna SD, Zhang Y, Briggs SD, Li J, Eissenberg JC, Allis CD, Khorasanizadeh S (2001) Specificity of the HP1 chromo domain for the methylated N-terminus of histone H3. EMBO J 20: 5232-5241
72. Jia S, Noma K, Grewal SI (2004) RNAi-independent heterochromatin nucleation by the stress-activated ATF/CREB family proteins. Science 304: 1971-1976
73. Kanoh J, Ishikawa F (2001) spRap1 and spRif1, recruited to telomeres by Taz1, are essential for telomere function in fission yeast. Curr Biol 11: 1624-1630
74. Kanoh J, Sadaie M, Urano T, Ishikawa F (2005) Telomere binding protein Taz1 establishes Swi6 heterochromatin independently of RNAi at telomeres. Curr Biol 15: 1808-1819
75. Kato H, Goto DB, Martienssen RA, Urano T, Furukawa K, Murakami Y (2005) RNA polymerase II is required for RNAi-dependent heterochromatin assembly. Science 309: 467-469
76. Konig P, Rhodes D (1997) Recognition of telomeric DNA. Trends Biochem Sci 22: 43-47
77. Larose S, Laterreur N, Ghazal G, Gagnon J, Wellinger RJ, Elela SA (2007) RNase III-dependent regulation of yeast telomerase. J Biol Chem 282: 4373-4381
78. Leeb M, Steffen PA, Wutz A (2009) X chromosome inactivation sparked by non-coding RNAs. RNA Biol 6 (E-pub ahead of print)
79. Liaw H, Lustig AJ (2006) Sir3 C-terminal domain involvement in the initiation and spreading of heterochromatin. Mol Cell Biol 26: 7616-7631
80. Liou GG, Tanny JC, Kruger RG, Walz T, Moazed D (2005) Assembly of the SIR complex and its regulation by O-acetyl-ADP-ribose, a product of NAD-dependent histone deacetylation. Cell 121: 515-527
81. Loo S, Rine J (1994) Silencers and domains of generalized repression. Science 264: 1768-1771
82. Louis EJ, Haber JE (1992) The structure and evolution of subtelomeric Y′ repeats in Saccharomyces cerevisiae. Genetics 131: 559-574
83. Luke B, Lingner J (in press) TERRA-Telomeric Repeat Containing RNA. EMBO J
84. Luke B, Panza A, Redon S, Iglesias N, Li Z, Lingner J (2008) The Rat1p 5′ to 3′ exonuclease degrades telomeric repeat-containing RNA and promotes telomere elongation in Saccharomyces cerevisiae. Mol Cell 32: 465-477
85. Luo K, Vega-Palas MA, Grunstein M (2002) Rap1-Sir4 binding independent of other Sir, yKu, or histone interactions initiates the assembly of telomeric heterochromatin in yeast. Genes Dev 16: 1528-1539
86. Maillet L, Boscheron C, Gotta M, Marcand S, Gilson E, Gasser SM (1996) Evidence for silencing compartments within the yeast nucleus: a role for telomere proximity and Sir protein concentration in silencer-mediated repression. Genes Dev 10: 1796-1811
87. Maillet L, Gaden F, Brevet V, Fourel G, Martin SG, Dubrana K, Gasser SM, Gilson E (2001) Ku-deficient yeast strains exhibit alternative states of silencing competence. EMBO Rep 2: 203-210
88. Mandell JG, Bahler J, Volpe TA, Martienssen RA, Cech TR (2005) Global expression changes resulting from loss of telomeric DNA in fission yeast. Genome Biol 6: R1
89. Martens JA, Laprade L, Winston F (2004) Intergenic transcription is required to repress the Saccharomyces cerevisiae SER3 gene. Nature 429: 571-574
90. Martin SG, Laroche T, Suka N, Grunstein M, Gasser SM (1999) Relocalization of telomeric Ku and SIR proteins in response to DNA strand breaks in yeast. Cell 97: 621-633
91. Martino F, Kueng S, Robinson P, Tsai-Pflugfelder M, van Leeuwen F, Ziegler M, Cubizolles F, Cockell MM, Rhodes D, Gasser SM (2009) Reconstitution of yeast silent chromatin: multiple contact sites and O-AADPR binding load SIR complexes onto nucleosomes in vitro. Mol Cell 33: 323-334
92. Meluh PB, Yang P, Glowczewski L, Koshland D, Smith MM (1998) Cse4p is a component of the core centromere of Saccharomyces cerevisiae. Cell 94: 607-613
93. Mishra K, Shore D (1999) Yeast Ku protein plays a direct role in telomeric silencing and counteracts inhibition by Rif proteins. Curr Biol 9: 1123-1126
94. Moqtaderi Z, Struhl K (2004) Genome-wide occupancy profile of the RNA polymerase III machinery in Saccharomyces cerevisiae reveals loci with incomplete transcription complexes. Mol Cell Biol 24: 4118-4127
95. 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
96. Motamedi MR, Verdel A, Colmenares SU, Gerber SA, Gygi SP, Moazed D (2004) Two RNAi complexes, RITS and RDRC, physically interact and localize to noncoding centromeric RNAs. Cell 119: 789-802
97. Mourelatos Z, Dostie J, Paushkin S, Sharma A, Charroux B, Abel L, Rappsilber J, Mann M, Dreyfuss G (2002) miRNPs: a novel class of ribonucleoproteins containing numerous microRNAs. Genes Dev 16: 720-728
98. Muchardt C, Guilleme M, Seeler JS, Trouche D, Dejean A, Yaniv M (2002) Coordinated methyl and RNA binding is required for heterochromatin localization of mammalian HP1alpha. EMBO Rep 3: 975-981
99. Muller HJ (1930) Types of visible variations induced by X-rays in Drosophila. J Genet 22: 299-334
100. Murakami H, Goto DB, Toda T, Chen ES, Grewal SI, Martienssen RA, Yanagida M (2007) Ribonuclease activity of Dis3 is required for mitotic progression and provides a possible link between heterochromatin and kinetochore function. PLoS ONE 2: e317
101. Mythreye K, Bloom KS (2003) Differential kinetochore protein requirements for establishment versus propagation of centromere activity in Saccharomyces cerevisiae. J Cell Biol 160: 833-843
102. 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
103. Noma K, Cam HP, Maraia RJ, Grewal SI (2006) A role for TFIIIC transcription factor complex in genome organization. Cell 125: 859-872
104. Noma K, Sugiyama T, Cam H, Verdel A, Zofall M, Jia S, Moazed D, Grewal SI (2004) RITS acts in cis to promote RNA interference-mediated transcriptional and post-transcriptional silencing. Nat Genet 36: 1174-1180
105. Partridge JF, Borgstrom B, Allshire RC (2000) Distinct protein interaction domains and protein spreading in a complex centromere. Genes Dev 14: 783-791
106. Partridge JF, Scott KS, Bannister AJ, Kouzarides T, Allshire RC (2002) cis-acting DNA from fission yeast centromeres mediates histone H3 methylation and recruitment of silencing factors and cohesin to an ectopic site. Curr Biol 12: 1652-1660
107. Pidoux AL, Allshire RC (2004) Kinetochore and heterochromatin domains of the fission yeast centromere. Chromosome Res 12: 521-534
108. Pillai RS (2005) MicroRNA function: multiple mechanisms for a tiny RNA? RNA
109. Reinhart BJ, Bartel DP (2002) Small RNAs correspond to centromere heterochromatic repeats. Science 297: 1831
110. Rusche LN, Kirchmaier AL, Rine J (2003) The establishment, inheritance, and function of silenced chromatin in Saccharomyces cerevisiae. Annu Rev Biochem 72: 481-516
111. Sadaie M, Iida T, Urano T, Nakayama J (2004) A chromodomain protein, Chp1, is required for the establishment of heterochromatin in fission yeast. EMBO J 23: 3825-3835
112. Schober H, Ferreira H, Kalck V, Gehlen LR, Gasser SM (2009) Yeast telomerase and the SUN domain protein Mps3 anchor telomeres and repress subtelomeric recombination. Genes Dev 23: 928-938
113. Schoeftner S, Blasco MA (2008) Developmentally regulated transcription of mammalian telomeres by DNA-dependent RNA polymerase II. Nat Cell Biol 10: 228-236
114. Sekinger EA, Gross DS (2001) Silenced chromatin is permissive to activator binding and PIC recruitment. Cell 105: 403-414
115. Senner CE, Brockdorff N (2009) Xist gene regulation at the onset of X inactivation. Curr Opin Genet Dev 19: 122-126
116. Shankaranarayana GD, Motamedi MR, Moazed D, Grewal SI (2003) Sir2 regulates histone H3 lysine 9 methylation and heterochromatin assembly in fission yeast. Curr Biol 13: 1240-1246
117. Sijen T, Fleenor J, Simmer F, Thijssen KL, Parrish S, Timmons L, Plasterk RH, Fire A (2001) On the role of RNA amplification in dsRNA-triggered gene silencing. Cell 107: 465-476
118. Singh J, Klar AJ (1992) Active genes in budding yeast display enhanced in vivo accessibility to foreign DNA methylases: a novel in vivo probe for chromatin structure of yeast. Genes Dev 6: 186-196
119. Smith MM (2002) Centromeres and variant histones: what, where, when and why? Curr Opin Cell Biol 14: 279-285
120. Steiner NC, Clarke L (1994) A novel epigenetic effect can alter centromere function in fission yeast. Cell 79: 865-874
121. 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
122. Suka N, Suka Y, Carmen AA, Wu J, Grunstein M (2001) Highly specific antibodies determine histone acetylation site usage in yeast heterochromatin and euchromatin. Mol Cell 8: 473-479
123. Sullivan BA, Blower MD, Karpen GH (2001) Determining centromere identity: cyclical stories and forking paths. Nat Rev Genet 2: 584-596
124. Taddei A, Hediger F, Neumann FR, Bauer C, Gasser SM (2004) Separation of silencing from perinuclear anchoring functions in yeast Ku80, Sir4 and Esc1 proteins. EMBO J 23: 1301-1312
125. Taddei A, Van Houwe G, Nagai S, Erb I, van Nimwegen E, Gasser SM (2009) The functional importance of telomere clustering: Global changes in gene expression result from SIR factor dispersion. Genome Res 19: 611-625
126. Tanaka T, Cosma MP, Wirth K, Nasmyth K (1999) Identification of cohesin association sites at centromeres and along chromosome arms. Cell 98: 847-858
127. Tanner KG, Landry J, Sternglanz R, Denu JM (2000) Silent information regulator 2 family of NAD- dependent histone/protein deacetylases generates a unique product, 1-O-acetyl-ADP-ribose. Proc Natl Acad Sci USA 97: 14178-14182
128. Tanny JC, Dowd GJ, Huang J, Hilz H, Moazed D (1999) An enzymatic activity in the yeast Sir2 protein that is essential for gene silencing. Cell 99: 735-745
129. Tanny JC, Moazed D (2001) Coupling of histone deacetylation to NAD breakdown by the yeast silencing protein Sir2: evidence for acetyl transfer from substrate to an NAD breakdown product. Proc Natl Acad Sci USA 98: 415-420
130. Thompson JS, Ling X, Grunstein M (1994) Histone H3 amino terminus is required for telomeric and silent mating locus repression in yeast. Nature 369: 245-247
131. Thon G, Verhein-Hansen J (2000) Four chromo-domain proteins of Schizosaccharomyces pombe differentially repress transcription at various chromosomal locations. Genetics 155: 551-568
132. Torras-Llort M, Moreno-Moreno O, Azorin F (2009) Focus on the centre: the role of chromatin on the regulation of centromere identity and function. EMBO J (e-pub ahead of print 23 July 2009; doi:10.1038/emboj.2009.174)
133. Uetz P, Giot L, Cagney G, Mansfield TA, Judson RS, Knight JR, Lockshon D, Narayan V, Srinivasan M, Pochart P, Qureshi-Emili A, Li Y, Godwin B, Conover D, Kalbfleisch T, Vijayadamodar G, Yang M, Johnston M, Fields S, Rothberg JM (2000) A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 403: 623-627
134. van Leeuwen F, Gafken PR, Gottschling DE (2002) Dot1p modulates silencing in yeast by methylation of the nucleosome core. Cell 109: 745-756
135. Vasiljeva L, Kim M, Terzi N, Soares LM, Buratowski S (2008) Transcription termination and RNA degradation contribute to silencing of RNA polymerase II transcription within heterochromatin. Mol Cell 29: 313-323
136. Vega-Palas MA, Venditti S, Di Mauro E (1998) Heterochromatin organization of a natural yeast telomere. Changes of nucleosome distribution driven by the absence of Sir3p. J Biol Chem 273: 9388-9392
137. 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
138. 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
139. Wakimoto BT (1998) Beyond the nucleosome: epigenetic aspects of position-effect variegation in Drosophila. Cell 93: 321-324
140. Wang SW, Stevenson AL, Kearsey SE, Watt S, Bahler J (2008) Global role for polyadenylation-assisted nuclear RNA degradation in posttranscriptional gene silencing. Mol Cell Biol 28: 656-665
141. Wiren M, Silverstein RA, Sinha I, Walfridsson J, Lee HM, Laurenson P, Pillus L, Robyr D, Grunstein M, Ekwall K (2005) Genomewide analysis of nucleosome density histone acetylation and HDAC function in fission yeast. EMBO J 24: 2906-2918
142. Wood V, Gwilliam R, Rajandream MA, Lyne M, Lyne R, Stewart A, Sgouros J, Peat N, Hayles J, Baker S, Basham D, Bowman S, Brooks K, Brown D, Brown S, Chillingworth T, Churcher C, Collins M, Connor R, Cronin A et al. (2002) The genome sequence of Schizosaccharomyces pombe. Nature 415: 871-880
143. Wyers F, Rougemaille M, Badis G, Rousselle JC, Dufour ME, Boulay J, Regnault B, Devaux F, Namane A, Seraphin B, Libri D, Jacquier A (2005) Cryptic Pol II transcripts are degraded by a nuclear quality control pathway involving a new Poly(A) polymerase. Cell 121: 725-737
144. Yamada M, Hayatsu N, Matsuura A, Ishikawa F (1998) Y′-Help1, a DNA helicase encoded by the yeast subtelomeric Y′ element, is induced in survivors defective for telomerase. J Biol Chem 273: 33360-33366
145. 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
146. Zakian VA (1996) Structure, function, and replication of Saccharomyces cerevisiae telomeres. Annu Rev Genet 30: 141-172
147. Zamore PD (2001) RNA interference: listening to the sound of silence. Nat Struct Biol 8: 746-750
148. Zaratiegui M, Irvine DV, Martienssen RA (2007) Noncoding RNAs and gene silencing. Cell 128: 763-776
149. Zhang K, Mosch K, Fischle W, Grewal SI (2008) Roles of the Clr4 methyltransferase complex in nucleation, spreading and maintenance of heterochromatin. Nat Struct Mol Biol 15: 381-388
150. Zhu C, Byers KJ, McCord RP, Shi Z, Berger MF, Newburger DE, Saulrieta K, Smith Z, Shah MV, Radhakrishnan M, Philippakis AA, Hu Y, De Masi F, Pacek M, Rolfs A, Murthy T, Labaer J, Bulyk ML (2009) High-resolution DNA-binding specificity analysis of yeast transcription factors. Genome Res 19: 556-566