SIR proteins and the assembly of silent chromatin in budding yeast

Annual Review of Genetics

Volumn 47, Issue , 2013, Pages 275-306

  Kueng, Stephanie ^a,c   Oppikofer, Mariano ^a,b,d   Gasser, Susan M ^a,b  

^a FRIEDRICH MIESCHER INSTITUTE FOR BIOMEDICAL RESEARCH   (Switzerland)

^b UNIVERSITY OF BASEL   (Switzerland)

^c F HOFFMANN LA ROCHE LTD   (Switzerland)

^d GENENTECH INC   (United States)

Author keywords

Mating type; S cerevisiae; Sir2; Sir3; Sir4; Telomere

Indexed keywords

SILENT INFORMATION REGULATOR PROTEIN; SILENT INFORMATION REGULATOR PROTEIN 2; SILENT INFORMATION REGULATOR PROTEIN 3; SILENT INFORMATION REGULATOR PROTEIN 4; UNCLASSIFIED DRUG;

CHROMATIN; CHROMATIN ASSEMBLY AND DISASSEMBLY; EPIGENETIC REPRESSION; GENE REPRESSION; GENE SILENCING; GENETIC ASSOCIATION; HETEROCHROMATIN; NONHUMAN; NUCLEOSOME; PRIORITY JOURNAL; REVIEW; SACCHAROMYCES CEREVISIAE; SILENCER ELEMENT; TELOMERE; YEAST;

EUKARYOTA; SACCHAROMYCES CEREVISIAE; SACCHAROMYCETALES;

ACETYLATION; CHROMATIN; DNA, FUNGAL; GENE SILENCING; GENES, FUNGAL; HETEROCHROMATIN; HISTONES; HOMEODOMAIN PROTEINS; MODELS, GENETIC; NUCLEOSOMES; PROTEIN BINDING; PROTEIN PROCESSING, POST-TRANSLATIONAL; PROTEIN STRUCTURE, TERTIARY; REPRESSOR PROTEINS; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; SILENT INFORMATION REGULATOR PROTEINS, SACCHAROMYCES CEREVISIAE; TELOMERE; TRANSCRIPTION FACTORS; TRANSCRIPTION, GENETIC;

EID: 84881238330     PISSN: 00664197     EISSN: 15452948     Source Type: Book Series    
DOI: 10.1146/annurev-genet-021313-173730     Document Type: Review

References (258)

1. Abraham J, Nasmyth KA, Strathern JN, Klar AJ, Hicks JB. 1984. Regulation of mating-type information in yeast. Negative control requiring sequences both 5' and 3 to the regulated region. J. Mol. Biol. 176:307-31
2. Altaf M, Utley RT, Lacoste N, Tan S, Briggs SD, Cote J. 2007. Interplay of chromatin modifiers on a short basic patch of histone H4 tail defines the boundary of telomeric heterochromatin. Mol. Cell 28:1002-14
3. Anastasia SD, Nguyen DL, Thai V, Meloy M, MacDonough T, Kellogg DR. 2012. A link between mitotic entry and membrane growth suggests a novel model for cell size control. J. Cell Biol. 197:89-104
4. Andrulis ED, Neiman AM, Zappulla DC, Sternglanz R. 1998. Perinuclear localization of chromatin facilitates transcriptional silencing. Nature 394:592-95
5. Andrulis ED, Zappulla DC, Alexieva-Botcheva K, Evangelista C, Sternglanz R. 2004. One-hybrid screens at the Saccharomyces cerevisiae HMR locus identify novel transcriptional silencing factors. Genetics 166:631-35
6. Andrulis ED, Zappulla DC, Ansari A, Perrod S, Laiosa CV, et al. 2002. Esc1, a nuclear periphery protein required for Sir4-based plasmid anchoring and partitioning. Mol. Cell. Biol. 22:8292-301
7. Ansari A, Gartenberg MR. 1999. Persistence of an alternate chromatin structure at silenced loci in vitro. Proc. Natl. Acad. Sci. USA 96:343-48
8. 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
9. Aparicio OM, Billington BL, Gottschling DE. 1991. Modifiers of position effect are shared between telomeric and silent mating-type loci in S cerevisiae. Cell 66:1279-87
10. Armache KJ, Garlick JD, Canzio D, Narlikar GJ, Kingston RE. 2011. Structural basis of silencing: Sir3 BAH domain in complex with a nucleosome at 3.0 A resolution. Science 334:977-82
11. Armstrong CM, Kaeberlein M, Imai SI, Guarente L. 2002. Mutations in Saccharomyces cerevisiae gene SIR2 can have differential effects on in vivo silencing phenotypes and in vitro histone deacetylation activity. Mol. Biol. Cell 13:1427-38
12. Arnaudo N, Fernández IS, McLaughlin SH, Peak-Chew SJ, Rhodes D, Martino F. 2013. The N-terminal acetylation of Sir3 stabilizes its binding to the nucleosome core particle. Nat. Struct. Mol. Biol. 20:1119-21
13. Bell SD, Botting CH, Wardleworth BN, Jackson SP, White MF. 2002. The interaction of Alba, a conserved archaeal chromatin protein, with Sir2 and its regulation by acetylation. Science 296:148-51
14. Bell SP, Mitchell J, Leber J, Kobayashi R, Stillman B. 1995. The multidomain structure of Orc1p reveals similarity to regulators of DNA replication and transcriptional silencing. Cell 83:563-68
15. Bheda P, Swatkoski S, Fiedler KL, Boeke JD, Cotter RJ, Wolberger C. 2012. Biotinylation of lysine method identifies acetylated histone H3 lysine 79 in Saccharomyces cerevisiae as a substrate for Sir2. Proc. Natl. Acad. Sci. USA 109:E916-25
16. Bi X, Broach JR. 1999. UASrpg can function as a heterochromatin boundary element in yeast. Genes Dev. 13:1089-101
17. Bitterman KJ, Anderson RM, Cohen HY, Latorre-Esteves M, Sinclair DA. 2002. Inhibition of silencing and accelerated aging by nicotinamide, a putative negative regulator of yeast sir2 and human SIRT1. J. Biol. Chem. 277:45099-107
18. +-dependent histone/protein deacetylases. Biochemistry 43:9877-87
19. Brand AH, Breeden L, Abraham J, Sternglanz R, Nasmyth K. 1985. Characterization of a "silencer" in yeast: a DNA sequence with properties opposite to those of a transcriptional enhancer. Cell 41:41-48
20. Brand AH, Micklem G, Nasmyth K. 1987. A yeast silencer contains sequences that can promote autonomous plasmid replication and transcriptional activation. Cell 51:709-19
21. Braunstein M, Rose AB, Holmes SG, Allis CD, Broach JR. 1993. Transcriptional silencing in yeast is associated with reduced nucleosome acetylation. Genes Dev. 7:592-604
22. Buchberger JR, Onishi M, Li G, Seebacher J, Rudner AD, et al. 2008. Sir3-nucleosome interactions in spreading of silent chromatin in Saccharomyces cerevisiae. Mol. Cell. Biol. 28:6903-18
23. Buchman AR, Kimmerly WJ, Rine J, Kornberg RD. 1988. Two DNA-binding factors recognize specific sequencesatsilencers, upstream activating sequences, autonomously replicating sequences, and telomeres in Saccharomyces cerevisiae. Mol. Cell. Biol. 8:210-25
24. 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. 9:370-84
25. Bupp JM, Martin AE, Stensrud ES, Jaspersen SL. 2007. Telomere anchoring at the nuclear periphery requires the budding yeast Sad1-UNC-84 domain protein Mps3. J. Cell Biol. 179:845-54
26. Chan JN, Poon BP, Salvi J, Olsen JB, Emili A, Mekhail K. 2011. Perinuclear cohibin complexes maintain replicative life span via roles at distinct silent chromatin domains. Dev. Cell 20:867-79
27. Chang JF, Hall BE, Tanny JC, Moazed D, Filman D, Ellenberger T. 2003. Structure of the coiled-coil dimerization motif of Sir4 and its interaction with Sir3. Structure 11:637-49
28. Chen L, Widom J. 2005. Mechanism of transcriptional silencing in yeast. Cell 120:37-48
29. Chen Y, Rai R, Zhou ZR, Kanoh J, Ribeyre C, et al. 2011. A conserved motif within RAP1 has diversified roles in telomere protection and regulation in different organisms. Nat. Struct. Mol. Biol. 18:213-21
30. Cheng TH, Gartenberg MR. 2000. Yeast heterochromatin is a dynamic structure that requires silencers continuously. Genes Dev. 14:452-63
31. 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 95:5521-26
32. Chien CT, Buck S, Sternglanz R, Shore D. 1993. Targeting of SIR1 protein establishes transcriptional silencing at HM loci and telomeres in yeast. Cell 75:531-41
33. Chou CC, Li YC, Gartenberg MR. 2008. Bypassing Sir2 and O-acetyl-ADP-ribose in transcriptional silencing. Mol. Cell 31:650-59
34. 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. 63:401-12
35. Cockell M, Palladino F, Laroche T, Kyrion G, Liu C, et al. 1995. The carboxy termini of Sir4 and Rap1 affect Sir3 localization: evidence for a multicomponent complex required for yeast telomeric silencing. J. Cell Biol. 129:909-24
36. Cockell MM, Perrod S, Gasser SM. 2000. Analysis of Sir2p domains required for rDNA and telomeric silencing in Saccharomyces cerevisiae. Genetics 154:1069-83
37. Connelly JJ, Yuan P, Hsu HC, Li Z, Xu RM, Sternglanz R. 2006. Structure and function of the Saccha-romyces cerevisiae Sir3 BAH domain. Mol. Cell. Biol. 26:3256-65
38. Conrad MN, Wright JH, Wolf AJ, Zakian VA. 1990. RAP1 protein interacts with yeast telomeres in vivo: overproduction alters telomere structure and decreases chromosome stability. Cell 63:739-50
39. Cubizolles F, Gasser SM. 2001. The nucleosome: from wallflower to queen of the ball. Genome Biol. 2:reports4023
40. Cubizolles F, Martino F, Perrod S, Gasser SM. 2006. A homotrimer-heterotrimer switchinSir2 structure differentiates rDNA and telomeric silencing. Mol. Cell 21:825-36
41. Cuperus G, Shafaatian R, Shore D. 2000. Locus specificity determinants in the multifunctional yeast silencing protein Sir2. EMBO J. 19:2641-51
42. Cuperus G, Shore D. 2002. Restoration of silencing in Saccharomyces cerevisiae by tethering of a novel Sir2-interacting protein, Esc8. Genetics 162:633-45
43. de Bruin D, Kantrow SM, Liberatore RA, Zakian VA. 2000. Telomere folding is required for the stable maintenance of telomere position effects in yeast. Mol. Cell. Biol. 20:7991-8000
44. de Bruin D, Zaman Z, Liberatore RA, Ptashne M. 2001. Telomere looping permits gene activation by a downstream UAS in yeast. Nature 409:109-13
45. Dernburg AF, Broman KW, Fung JC, Marshall WF, Philips J, et al. 1996. Perturbation of nuclear architecture by long-distance chromosome interactions. Cell 85:745-59
46. Dhillon N, Kamakaka RT. 2000. A histone variant, Htz1p, and a Sir1p-like protein, Esc2p, mediate silencing at HMR. Mol. Cell 6:769-80
47. Diffley JF, Stillman B. 1989. Similarity between the transcriptional silencer binding proteins ABF1 and RAP1. Science 246:1034-38
48. Dion MF, Kaplan T, Kim M, Buratowski S, Friedman N, Rando OJ. 2007. Dynamics of replication-independent histone turnover in budding yeast. Science 315:1405-8
49. Donze D, Kamakaka RT. 2001. RNA polymerase III and RNA polymerase II promoter complexes are heterochromatin barriers in Saccharomyces cerevisiae. EMBO J. 20:520-31
50. Dubarry M, Loiodice I, Chen CL, Thermes C, Taddei A. 2011. Tight protein-DNA interactions favor gene silencing. Genes Dev. 25:1365-70
51. Ehrenhofer-Murray AE, Rivier DH, Rine J. 1997. The role of Sas2, an acetyltransferase homologue of Saccharomyces cerevisiae, in silencing and ORC function. Genetics 145:923-34
52. + domain in silencing: interaction with Sir4 and unmethylated histone H3K79. Genes Dev. 25:1835-46
53. Emre NC, Ingvarsdottir K, Wyce A, Wood A, Krogan NJ, et al. 2005. Maintenance of low histone ubiquitylation by Ubp10 correlates with telomere-proximal Sir2 association and gene silencing. Mol. Cell 17:585-94
54. Enomoto S, Johnston SD, Berman J. 2000. Identification of a novel allele of SIR3 defective in the maintenance, but not the establishment, of silencing in Saccharomyces cerevisiae. Genetics 155:523-38
55. Enomoto S, Longtine MS, Berman J. 1994. Enhancement of telomere-plasmid segregation by the X-telomere associated sequence in Saccharomyces cerevisiae involves SIR2, SIR3, SIR4 and ABF1. Genetics 136:757-67
56. Feeser EA, Wolberger C. 2008. Structural and functional studies of the Rap1 C-terminus reveal novel separation-of-function mutants. J. Mol. Biol. 380:520-31
57. Feldman JB, Hicks JB, Broach JR. 1984. Identification of sites required for repression of a silent mating type locus in yeast. J. Mol. Biol. 178:815-34
58. Ferreira HC, Luke B, Schober H, Kalck V, Lingner J, Gasser SM. 2011. The PIAS homologue Siz2 regulates perinuclear telomere position and telomerase activity inbudding yeast. Nat. Cell Biol. 13:867-74
59. Fierz B, Chatterjee C, McGinty RK, Bar-Dagan M, Raleigh DP, Muir TW. 2011. Histone H2B ubiq-uitylation disrupts local and higher-order chromatin compaction. Nat. Chem. Biol. 7:113-19
60. Finnin MS, Donigian JR, Pavletich NP. 2001. Structure of the histone deacetylase SIRT2. Nat. Struct. Biol. 8:621-25
61. Foster ER, Downs JA. 2009. Methylation of H3 K4 and K79 is not strictly dependent on H2B K123 ubiquitylation. J. Cell Biol. 184:631-38
62. Fourel G, Boscheron C, Revardel E, Lebrun E, Hu YF, et al. 2001. An activation-independent role of transcription factors in insulator function. EMBO Rep. 2:124-32
63. Fourel G, Lebrun E, Gilson E. 2002. Protosilencers as building blocks for heterochromatin. Bioessays 24:828-35
64. Fourel G, Magdinier F, Gilson E. 2004. Insulator dynamics and the setting of chromatin domains. Bioessays 26:523-32
65. Fourel G, Revardel E, Koering CE, Gilson E. 1999. Cohabitation of insulators and silencing elements in yeast subtelomeric regions. EMBO J. 18:2522-37
66. Froyd CA, Rusche LN. 2011. The duplicated deacetylases Sir2 and Hst1 subfunctionalized by acquiring complementary inactivating mutations. Mol. Cell. Biol. 31:3351-65
67. Frye RA. 2000. Phylogenetic classification of prokaryotic and eukaryotic Sir2-like proteins. Biochem. Biophys. Res. Commun. 273:793-98
68. Gao L, Gross DS. 2006. Using genomics and proteomics to investigate mechanisms of transcriptional silencing in Saccharomyces cerevisiae. Brief Funct. Genomic Proteomic 5:280-88
69. Gao L, Gross DS. 2008. Sir2 silences gene transcription by targeting the transition between RNA polymerase II initiation and elongation. Mol. Cell. Biol. 28:3979-94
70. Garbett KA, Tripathi MK, Cencki B, Layer JH, Weil PA. 2007. Yeast TFIID serves as a coactivator for Rap1p by direct protein-protein interaction. Mol. Cell. Biol. 27:297-311
71. Garcia SN, Pillus L. 2002. A unique class of conditional sir2 mutants displays distinct silencing defects in Saccharomyces cerevisiae. Genetics 162:721-36
72. Gardner RG, Nelson ZW, Gottschling DE. 2005. Ubp10/Dot4p regulates the persistence of ubiquiti-nated histone H2B: distinct roles in telomeric silencing and general chromatin. Mol. Cell. Biol. 25:6123-39
73. Gartenberg MR, Neumann FR, Laroche T, Blaszczyk M, Gasser SM. 2004. Sir-mediated repression can occur independently of chromosomal and subnuclear contexts. Cell 119:955-67
74. Gasser SM, Cockell MM. 2001. The molecular biology of the SIR proteins. Gene 279:1-16
75. Geissenhoner A, Weise C, Ehrenhofer-Murray AE. 2004. Dependence of ORC silencing function on NatA-mediated Nα acetylation in Saccharomyces cerevisiae. Mol. Cell. Biol. 24:10300-12
76. Georgel PT, Palacios DeBeer MA, Pietz G, Fox CA, Hansen JC. 2001. Sir3-dependent assembly of supramolecular chromatin structures in vitro. Proc. Natl. Acad. Sci. USA 98:8584-89
77. Ghidelli S, Donze D, Dhillon N, Kamakaka RT. 2001. Sir2p exists in two nucleosome-binding complexes with distinct deacetylase activities. EMBO J. 20:4522-35
78. Gotta M, Laroche T, Formenton A, Maillet L, Scherthan H, Gasser SM. 1996. The clustering of telomeres and colocalization with Rap1, Sir3, and Sir4 proteins in wild-type Saccharomyces cerevisiae. J. Cell Biol. 134:1349-63
79. Gotta M, Palladino F, Gasser SM. 1998. Functional characterization of the N terminus of Sir3p. Mol. Cell. Biol. 18:6110-20
80. Gotta M, Strahl-Bolsinger S, Renauld H, Laroche T, Kennedy BK, et al. 1997. Localization of Sir2p: the nucleolus as a compartment for silent information regulators. EMBO J. 16:3243-55
81. Gottlieb S, Esposito RE. 1989. A new role for a yeast transcriptional silencer gene, SIR2, in regulation of recombination in ribosomal DNA. Cell 56:771-76
82. Gottschling DE. 1992. Telomere-proximal DNA in Saccharomyces cerevisiae is refractory to methyltrans-ferase activity in vivo. Proc. Natl. Acad. Sci. USA 89:4062-65
83. Gottschling DE, Aparicio OM, Billington BL, Zakian VA. 1990. Position effect at S cerevisiae telomeres: reversible repression of Pol II transcription. Cell 63:751-62
84. Gravel S, Larrivee M, Labrecque P, Wellinger RJ. 1998. Yeast Ku as a regulator of chromosomal DNA end structure. Science 280:741-44
85. Greiss S, Gartner A. 2009. Sirtuin/Sir2 phylogeny, evolutionary considerations and structural conservation. Mol. Cells 28:407-15
86. Grunweller A, Ehrenhofer-Murray AE. 2002. A novel yeast silencer. The 2mu origin of Saccharomyces cerevisiae has HST3-, MIG1-and SIR-dependent silencing activity. Genetics 162:59-71
87. Haber JE, George JP. 1979. A mutation that permits the expression of normally silent copies of mating-type information in Saccharomyces cerevisiae. Genetics 93:13-35
88. Harashima S, Nogi Y, Oshima Y. 1974. The genetic system controlling homothallism in Saccharomyces yeasts. Genetics 77:639-50
89. 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 80:583-92
90. Hecht A, Strahl-Bolsinger S, Grunstein M. 1996. Spreading of transcriptional repressor SIR3 from telomeric heterochromatin. Nature 383:92-96
91. 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. 12:2076-89
92. Hickman M, McCullough K, Woike A, Raducha-Grace L, Rozario T, et al. 2007. Isolation and characterization of conditional alleles of the yeast SIR2 gene. J. Mol. Biol. 367:1246-57
93. Hickman MA, Froyd CA, Rusche LN. 2011. Reinventing heterochromatin in budding yeasts: Sir2 and the origin recognition complex take center stage. Eukaryot. Cell 10:1183-92
94. Hickman MA, Rusche LN. 2007. Substitution as a mechanism for genetic robustness: the duplicated deacetylases Hst1p and Sir2p in Saccharomyces cerevisiae. PLoS Genet. 3:e126
95. Hickman MA, Rusche LN. 2010. Transcriptional silencing functions of the yeast protein Orc1/Sir3 subfunctionalized after gene duplication. Proc. Natl. Acad. Sci. USA 107:19384-89
96. Hicks J, Strathern JN. 1977. Interconversion of mating type in S cerevisiae and the cassette model for gene transfer. Brookhaven Symp. Biol. 29:233-42
97. Hiraga S, Robertson ED, Donaldson AD. 2006. The Ctf18 RFC-like complex positions yeast telomeres but does not specify their replication time. EMBO J. 25:1505-14
98. Hofmann JF, Laroche T, Brand AH, Gasser SM. 1989. RAP-1 factor is necessary for DNA loop formation in vitro at the silent mating type locus HML. Cell 57:725-37
99. Hoppe GJ, Tanny JC, Rudner AD, Gerber SA, Danaie S, et al. 2002. Steps in assembly of silent chromatin in yeast: Sir3-independent binding of a Sir2/Sir4 complex to silencers and role for Sir2-dependent deacetylation. Mol. Cell. Biol. 22:4167-80
100. Hsu HC, Wang CL, Wang M, Yang N, Chen Z, et al. 2013. Structural basis for allosteric stimulation of Sir2 activity by Sir4 binding. Genes Dev. 27:64-73
101. 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
102. Irlbacher H, Franke J, Manke T, Vingron M, Ehrenhofer-Murray AE. 2005. Control of replication initiation and heterochromatin formation in Saccharomyces cerevisiae by a regulator of meiotic gene expression. Genes Dev. 19:1811-22
103. Ishii K, Arib G, Lin C, Van Houwe G, Laemmli UK. 2002. Chromatin boundaries in budding yeast: the nuclear pore connection. Cell 109:551-62
104. Ivessa AS, Lenzmeier BA, Bessler JB, Goudsouzian LK, Schnakenberg SL, Zakian VA. 2003. The Sac-charomyces cerevisiae helicase Rrm3p facilitates replication past nonhistone protein-DNA complexes. Mol. Cell 12:1525-36
105. Johnson A, Li G, Sikorski TW, Buratowski S, Woodcock CL, Moazed D. 2009. Reconstitution of heterochromatin-dependent transcriptional gene silencing. Mol. Cell 35:769-81
106. Johnson LM, Kayne PS, Kahn ES, Grunstein M. 1990. Genetic evidence for an interaction between SIR3 and histone H4 in the repression of the silent mating loci in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 87:6286-90
107. Kaeberlein M, McVey M, Guarente L. 1999. The SIR2/3/4 complex and SIR2 alone promote longevity in Saccharomyces cerevisiae by two different mechanisms. Genes Dev. 13:2570-80
108. Kahana A, Gottschling DE. 1999. DOT4 links silencing and cell growth in Saccharomyces cerevisiae. Mol. Cell. Biol. 19:6608-20
109. Katan-Khaykovich Y, Struhl K. 2005. Heterochromatin formation involves changes in histone modifications over multiple cell generations. EMBO J. 24:2138-49
110. Kellis M, Birren BW, Lander ES. 2004. Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae. Nature 428:617-24
111. Kennedy BK, Gotta M, Sinclair DA, Mills K, McNabb DS, et al. 1997. Redistribution of silencing proteins from telomeres to the nucleolus is associated with extension of life span in S cerevisiae. Cell 89:381-91
112. Keogh MC, Kim JA, Downey M, Fillingham J, Chowdhury D, et al. 2006. A phosphatase complex that dephosphorylates γH2AX regulates DNA damage checkpoint recovery. Nature 439:497-501
113. Kimmerly W, Buchman A, Kornberg R, Rine J. 1988. Roles of two DNA-binding factors in replication, segregation and transcriptional repression mediated by a yeast silencer. EMBO J. 7:2241-53
114. Kimura A, Umehara T, Horikoshi M. 2002. Chromosomal gradient of histone acetylation established by Sas2p and Sir2p functions as a shield against gene silencing. Nat. Genet. 32:370-77
115. King DA, Hall BE, Iwamoto MA, Win KZ, Chang JF, Ellenberger T. 2006. Domain structure and protein interactions of the silent information regulator Sir3 revealed by screening a nested deletion library of protein fragments. J. Biol. Chem. 281:20107-19
116. Kirchmaier AL, Rine J. 2006. Cell cycle requirements in assembling silent chromatin in Saccharomyces cerevisiae. Mol. Cell. Biol. 26:852-62
117. Kitada T, Kuryan BG, Tran NN, Song C, Xue Y, et al. 2012. Mechanism for epigenetic variegation of gene expression at yeast telomeric heterochromatin. Genes Dev. 26:2443-55
118. Kitada T, Schleker T, Sperling AS, Xie W, Gasser SM, Grunstein M. 2011. γH2A is a component of yeast heterochromatin required for telomere elongation. Cell Cycle 10:293-300
119. Klemm RD, Austin RJ, Bell SP. 1997. Coordinate binding of ATP and origin DNA regulates the ATPase activity of the origin recognition complex. Cell 88:493-502
120. Kueng S, Tsai-Pflugfelder M, Oppikofer M, Ferreira HC, Roberts E, et al. 2012. Regulating repression: roles for the sir4 N-terminus in linker DNA protection and stabilization of epigenetic states. PLoS Genet. 8:e1002727
121. Laroche T, Martin SG, Gotta M, Gorham HC, Pryde FE, et al. 1998. Mutation of yeast Ku genes disrupts the subnuclear organization of telomeres. Curr. Biol. 8:653-56
122. Laroche T, Martin SG, Tsai-Pflugfelder M, Gasser SM. 2000. The dynamics of yeast telomeres and silencing proteins through the cell cycle. J. Struct. Biol. 129:159-74
123. Lebrun E, Revardel E, Boscheron C, Li R, Gilson E, Fourel G. 2001. Protosilencers in Saccharomyces cerevisiae subtelomeric regions. Genetics 158:167-76
124. Lee JS, Shukla A, Schneider J, Swanson SK, Washburn MP, et al. 2007. Histone crosstalk between H2B monoubiquitination and H3 methylation mediated by COMPASS. Cell 131:1084-96
125. Leung A, Cajigas I, Jia P, Ezhkova E, Brickner JH, et al. 2011. Histone H2B ubiquitylation and H3 lysine 4 methylation prevent ectopic silencing of euchromatic loci important for the cellular response to heat. Mol. Biol. Cell 22:2741-53
126. Liaw H, Lustig AJ. 2006. Sir3 C-terminal domain involvement in the initiation and spreading of het-erochromatin. Mol. Cell. Biol. 26:7616-31
127. Lienert F, Wirbelauer C, Som I, Dean A, Mohn F, Schubeler D. 2011. Identification of genetic elements that autonomously determine DNA methylation states. Nat. Genet. 43:1091-97
128. Lin YY, Lu JY, Zhang J, Walter W, Dang W, et al. 2009. Protein acetylation microarray reveals that NuA4 controls key metabolic target regulating gluconeogenesis. Cell 136:1073-84
129. 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 121:515-27
130. Liu C, Lustig AJ. 1996. Genetic analysis of Rap1p/Sir3p interactions in telomeric and HML silencing in Saccharomyces cerevisiae. Genetics 143:81-93
131. Liu C, Mao X, Lustig AJ. 1994. Mutational analysis defines a C-terminal tail domain of RAP1 essential for telomeric silencing in Saccharomyces cerevisiae. Genetics 138:1025-40
132. Livi GP, Hicks JB, Klar AJ. 1990. The sum1-1 mutation affects silent mating-type gene transcription in Saccharomyces cerevisiae. Mol. Cell. Biol. 10:409-12
133. Loo S, Rine J. 1994. Silencers and domains of generalized repression. Science 264:1768-71
134. Louis EJ. 1995. The chromosome ends of Saccharomyces cerevisiae. Yeast 11:1553-73
135. 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. 16:1528-39
136. Lustig AJ, Liu C, Zhang C, Hanish JP. 1996. Tethered Sir3p nucleates silencing at telomeres and internal loci in Saccharomyces cerevisiae. Mol. Cell. Biol. 16:2483-95
137. Lynch PJ, Rusche LN. 2009. A silencer promotes the assembly of silenced chromatin independently of recruitment. Mol. Cell. Biol. 29:43-56
138. Lynch PJ, Rusche LN. 2010. An auxiliary silencer and a boundary element maintain high levels of silencing proteins at HMR in Saccharomyces cerevisiae. Genetics 185:113-27
139. Mackay V, Manney TR. 1974. Mutations affecting sexual conjugation and related processes in Saccha-romyces cerevisiae. II. Genetic analysis of nonmating mutants. Genetics 76:273-88
140. Mahoney DJ, Broach JR. 1989. The HML mating-type cassette of Saccharomyces cerevisiae is regulated by two separate but functionally equivalent silencers. Mol. Cell. Biol. 9:4621-30
141. 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. 10:1796-811
142. Maillet L, Gaden F, Brevet V, Fourel G, Martin SG, et al. 2001. Ku-deficient yeast strains exhibit alternative states of silencing competence. EMBO Rep. 2:203-10
143. Marcand S, Buck SW, Moretti P, Gilson E, Shore D. 1996. Silencing of genes at nontelomeric sites in yeast is controlled by sequestration of silencing factors at telomeres by Rap1 protein. Genes Dev. 10:1297-309
144. Marshall M, Mahoney D, Rose A, Hicks JB, Broach JR. 1987. Functional domains of SIR4, a gene required for position effect regulation in Saccharomyces cerevisiae. Mol. Cell. Biol. 7:4441-52
145. Martin-Morris LE, Csink AK, Dorer DR, Talbert PB, Henikoff S. 1997. Heterochromatic trans-inactivation of Drosophila white transgenes. Genetics 147:671-77
146. 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 97:621-33
147. Martino F, Kueng S, Robinson P, Tsai-Pflugfelder M, van Leeuwen F, et al. 2009. Reconstitution of yeast silent chromatin: multiple contact sites and O-AADPR binding load SIR complexes onto nucleosomes in vitro. Mol. Cell 33:323-34
148. Marvin ME, Griffin CD, Eyre DE, Barton DB, Louis EJ. 2009. In Saccharomyces cerevisiae, yKu and subtelomeric core X sequences repress homologous recombination near telomeres as part of the same pathway. Genetics 183:441-51, 1SI-12SI
149. Matecic M, Martins-Taylor K, Hickman M, Tanny J, Moazed D, Holmes SG. 2006. New alleles of SIR2 define cell-cycle-specific silencing functions. Genetics 173:1939-50
150. + concentration. J. Biol. Chem. 287:20957-66
151. McNally FJ, Rine J. 1991. A synthetic silencer mediates SIR-dependent functions in Saccharomyces cere-visiae. Mol. Cell. Biol. 11:5648-59
152. Mead J, McCord R, Youngster L, Sharma M, Gartenberg MR, Vershon AK. 2007. Swapping the gene-specific and regional silencing specificities of the Hst1 and Sir2 histone deacetylases. Mol. Cell. Biol. 27:2466-75
153. Meijsing SH, Ehrenhofer-Murray AE. 2001. The silencing complex SAS-I links histone acetylation to the assembly of repressed chromatin by CAF-I and Asf1 in Saccharomyces cerevisiae. Genes Dev. 15:3169-82
154. Mekhail K, Seebacher J, Gygi SP, Moazed D. 2008. Role for perinuclear chromosome tethering in maintenance of genome stability. Nature 456:667-70
155. Miele A, Bystricky K, Dekker J. 2009. Yeast silent mating type loci form heterochromatic clusters through silencer protein-dependent long-range interactions. PLoS Genet 5:e1000478
156. Min J, Landry J, Sternglanz R, Xu RM. 2001. Crystal structure of a SIR2 homolog-NAD complex. Cell 105:269-79
157. Mishra K, Shore D. 1999. Yeast Ku protein plays a direct role in telomeric silencing and counteracts inhibition by rif proteins. Curr. Biol. 9:1123-26
158. Moazed D. 2001. Common themes in mechanisms of gene silencing. Mol. Cell 8:489-98
159. Moazed D, Kistler A, Axelrod A, Rine J, Johnson AD. 1997. Silent information regulator protein complexes in Saccharomyces cerevisiae: a SIR2/SIR4 complex and evidence for a regulatory domain in SIR4 that inhibits its interaction with SIR3. Proc. Natl. Acad. Sci. USA 94:2186-91
160. Moazed D, Rudner AD, Huang J, Hoppe GJ, Tanny JC. 2004. A model for step-wise assembly of heterochromatin in yeast. Novartis Found. Symp. 259:48-56; discuss. 62, 163-69
161. Mondoux MA, Zakian VA. 2007. Subtelomeric elements influence but do not determine silencing levels at Saccharomyces cerevisiae telomeres. Genetics 177:2541-46
162. Moretti P, Freeman K, Coodly L, Shore D. 1994. Evidence that a complex of SIR proteins interacts with the silencer and telomere-binding protein RAP1. Genes Dev. 8:2257-69
163. Moretti P, Shore D. 2001. Multiple interactions in Sir protein recruitment by Rap1p at silencers and telomeres in yeast. Mol. Cell. Biol. 21:8082-94
164. Murphy GA, Spedale EJ, Powell ST, Pillus L, Schultz SC, Chen L. 2003. The Sir4 C-terminal coiled coil is required for telomeric and mating type silencing in Saccharomyces cerevisiae. J. Mol. Biol. 334:769-80
165. Onishi M, Liou GG, Buchberger JR, Walz T, Moazed D. 2007. Role of the conserved Sir3-BAH domain in nucleosome binding and silent chromatin assembly. Mol. Cell 28:1015-28
166. Oppikofer M, Kueng S, Keusch JJ, Hassler M, Ladurner AG, et al. 2013. Dimerization of Sir3 via its C-terminal winged helix domain is essential for yeast heterochromatin formation. EMBO J. 32:437-49
167. Oppikofer M, Kueng S, Martino F, Soeroes S, Hancock S, et al. 2011. The dual role of H4K16 acetylation in the establishment of yeast silent chromatin. EMBO J. 30:2610-21
168. Osborne EA, Dudoit S, Rine J. 2009. The establishment of gene silencing at single-cell resolution. Nat. Genet. 41:800-6
169. Ozaydin B, Rine J. 2010. Expanded roles of the origin recognition complex in the architecture and function of silenced chromatin in Saccharomyces cerevisiae. Mol. Cell. Biol. 30:626-39
170. Paetkau DW, Riese JA, MacMorran WS, Woods RA, Gietz RD. 1994. Interaction of the yeast RAD7 and SIR3 proteins: implications for DNA repair and chromatin structure. Genes Dev. 8:2035-45
171. Palladino F, Laroche T, Gilson E, Axelrod A, Pillus L, Gasser SM. 1993. SIR3 and SIR4 proteins are required for the positioning and integrity of yeast telomeres. Cell 75:543-55
172. Park EC, Szostak JW. 1992. ARD1 and NAT1 proteins form a complex that has N-terminal acetyltrans-ferase activity. EMBO J. 11:2087-93
173. Park JH, Cosgrove MS, Youngman E, Wolberger C, Boeke JD. 2002. A core nucleosome surface crucial for transcriptional silencing. Nat. Genet. 32:273-79
174. Pina B, Fernandez-Larrea J, Garcia-Reyero N, Idrissi FZ. 2003. The different (sur)faces of Rap1p. Mol. Genet. Genomics 268:791-98
175. ; elements in S cerevisiae suppress extreme variations in gene silencing. PLoS ONE 6:e17523
176. Prakash S, Prakash L. 2000. Nucleotide excision repair in yeast. Mutat. Res. 451:13-24
177. Pryde FE, Louis EJ. 1999. Limitations of silencing at native yeast telomeres. EMBO J. 18:2538-50
178. Radman-Livaja M, Ruben G, Weiner A, Friedman N, Kamakaka R, Rando OJ. 2011. Dynamics of Sir3 spreading in budding yeast: secondary recruitment sites and euchromatic localization. EMBO J. 30:1012-26
179. Rafty LA, Schmidt MT, Perraud AL, Scharenberg AM, Denu JM. 2002. Analysis of O-acetyl-ADP-ribose as a target for Nudix ADP-ribose hydrolases. J. Biol. Chem. 277:47114-22
180. Raghuraman MK, Brewer BJ, Fangman WL. 1997. Cell cycle-dependent establishment of a late replication program. Science 276:806-9
181. Ray A, Hector RE, Roy N, Song JH, Berkner KL, Runge KW. 2003. Sir3p phosphorylation by the Slt2p pathway effects redistribution of silencing function and shortened lifespan. Nat. Genet. 33:522-26
182. Reifsnyder C, Lowell J, Clarke A, Pillus L. 1996. Yeast SAS silencing genes and human genes associated with AML and HIV-1 Tat interactions are homologous with acetyltransferases. Nat. Genet. 14:42-49
183. Renauld H, Aparicio OM, Zierath PD, Billington BL, Chhablani SK, Gottschling DE. 1993. Silent domains are assembled continuously from the telomere and are defined by promoter distance and strength, and by SIR3 dosage. Genes Dev. 7:1133-45
184. Rine J, Herskowitz I. 1987. Four genes responsible for a position effect on expression from HML and HMR in Saccharomyces cerevisiae. Genetics 116:9-22
185. Rine J, Strathern JN, Hicks JB, Herskowitz I. 1979. A suppressor of mating-type locus mutations in Saccharomyces cerevisiae: evidence for and identification of cryptic mating-type loci. Genetics 93:877-901
186. Roy N, Runge KW. 1999. The ZDS1 and ZDS2 proteins require the Sir3p component of yeast silent chromatin to enhance the stability of short linear centromeric plasmids. Chromosoma 108:146-61
187. Roy N, Runge KW. 2000. Two paralogs involved intranscriptional silencing that antagonistically control yeast life span. Curr. Biol. 10:111-14
188. Roy R, Meier B, McAinsh AD, Feldmann HM, Jackson SP. 2004. Separation-of-function mutants of yeast Ku80 reveal a Yku80p-Sir4p interaction involved in telomeric silencing. J. Biol. Chem. 279:86-94
189. Ruault M, De Meyer A, Loiodice I, Taddei A. 2011. Clustering heterochromatin: Sir3 promotes telomere clustering independently of silencing in yeast. J. Cell Biol. 192:417-31
190. Rudner AD, Hall BE, Ellenberger T, Moazed D. 2005. A nonhistone protein-protein interaction required for assembly of the SIR complex and silent chromatin. Mol. Cell. Biol. 25:4514-28
191. Rusche LN, Kirchmaier AL, Rine J. 2002. Ordered nucleation and spreading of silenced chromatin in Saccharomyces cerevisiae. Mol. Biol. Cell 13:2207-22
192. Rusche LN, Kirchmaier AL, Rine J. 2003. The establishment, inheritance, and function of silenced chromatin in Saccharomyces cerevisiae. Annu. Rev. Biochem. 72:481-516
193. Sampath V, Yuan P, Wang IX, Prugar E, van Leeuwen F, Sternglanz R. 2009. Mutational analysis of the Sir3 BAH domain reveals multiple points of interaction with nucleosomes. Mol. Cell. Biol. 29:2532-45
194. Santos-Rosa H, Bannister AJ, Dehe PM, Geli V, Kouzarides T. 2004. Methylation of H3 lysine 4 at euchromatin promotes Sir3p association with heterochromatin. J. Biol. Chem. 279:47506-12
195. Sauve AA, Moir RD, Schramm VL, Willis IM. 2005. Chemical activation of Sir2-dependent silencing by relief of nicotinamide inhibition. Mol. Cell 17:595-601
196. Schmid M, Arib G, Laemmli C, Nishikawa J, Durussel T, Laemmli UK. 2006. Nup-PI: the nucleopore-promoter interaction of genes in yeast. Mol. Cell 21:379-91
197. 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. 23:928-38
198. Segal E, Fondufe-Mittendorf Y, Chen L, Thastrom A, Field Y, et al. 2006. A genomic code for nucleo-some positioning. Nature 442:772-78
199. Shia WJ, Li B, Workman JL. 2006. SAS-mediated acetylation of histone H4 Lys 16 is required for H2A.Z incorporation at subtelomeric regions in Saccharomyces cerevisiae. Genes Dev. 20:2507-12
200. Shore D, Nasmyth K. 1987. Purification and cloning of a DNA binding protein from yeast that binds to both silencer and activator elements. Cell 51:721-32
201. Shou W, Seol JH, Shevchenko A, Baskerville C, Moazed D, et al. 1999. Exit from mitosis is triggered by Tem1-dependent release of the protein phosphatase Cdc14 from nucleolar RENT complex. Cell 97:233-44
202. Singer MS, Gottschling DE. 1994. TLC1: template RNA component of Saccharomyces cerevisiae telom-erase. Science 266:404-9
203. 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. 6:186-96
204. Smith CD, Smith DL, DeRisi JL, Blackburn EH. 2003. Telomeric protein distributions and remodeling through the cell cycle in Saccharomyces cerevisiae. Mol. Biol. Cell 14:556-70
205. Smith JJ, Miller LR, Kreisberg R, Vazquez L, Wan Y, Aitchison JD. 2010. Environment-responsive transcription factors bind subtelomeric elements and regulate gene silencing. Mol. Syst. Biol. 7:455
206. Smith JS, Boeke JD. 1997. An unusual form of transcriptional silencing in yeast ribosomal DNA. Genes Dev. 11:241-54
207. +-dependent protein deacetylase activity in the Sir2 protein family. Proc. Natl. Acad. Sci. USA 97:6658-63
208. Smith JS, Brachmann CB, Pillus L, Boeke JD. 1998. Distribution of a limited Sir2 protein pool regulates the strength of yeast rDNA silencing and is modulated by Sir4p. Genetics 149:1205-19
209. Stavenhagen JB, Zakian VA. 1994. Internal tracts of telomeric DNA act as silencers in Saccharomyces cerevisiae. Genes Dev. 8:1411-22
210. Steinmetz EJ, Warren CL, Kuehner JN, Panbehi B, Ansari AZ, Brow DA. 2006. Genome-wide distribution of yeast RNA polymerase II and its control by Sen1 helicase. Mol. Cell 24:735-46
211. Stone EM, Reifsnyder C, McVey M, Gazo B, Pillus L. 2000. Two classes of sir3 mutants enhance the sir1 mutant mating defect and abolish telomeric silencing in Saccharomyces cerevisiae. Genetics 155:509-22
212. Strahl-Bolsinger S, Hecht A, Luo K, Grunstein M. 1997. SIR2 and SIR4 interactions differ in core and extended telomeric heterochromatin in yeast. Genes Dev. 11:83-93
213. Straight AF, Shou W, Dowd GJ, Turck CW, Deshaies RJ, et al. 1999. Net1, a Sir2-associated nucleolar protein required for rDNA silencing and nucleolar integrity. Cell 97:245-56
214. Stulemeijer IJ, Pike BL, Faber AW, Verzijlbergen KF, van Welsem T, et al. 2011. Dot1 binding induces chromatin rearrangements by histone methylation-dependent and-independent mechanisms. Epigenet. Chromatin 4:2
215. Suka N, Luo K, Grunstein M. 2002. Sir2p and Sas2p opposingly regulate acetylation of yeast histone H4 lysine16 and spreading of heterochromatin. Nat. Genet. 32:378-83
216. 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 8:473-79
217. Szilard RK, Jacques PE, Laramee L, Cheng B, Galicia S, et al. 2010. Systematic identification of fragile sites via genome-wide location analysis of γ-H2AX. Nat. Struct. Mol. Biol. 17:299-305
218. Taddei A, Gasser SM. 2004. Multiple pathways for telomere tethering: functional implications of sub-nuclear position for heterochromatin formation. Biochim. Biophys. Acta 1677:120-28
219. 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. 23:1301-12
220. 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. 19:611-25
221. Talbert PB, Henikoff S. 2000. A reexamination of spreading of position-effect variegation in the white-roughest region of Drosophila melanogaster. Genetics 154:259-72
222. 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 97:14178-82
223. 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 99:735-45
224. Tanny JC, Kirkpatrick DS, Gerber SA, Gygi SP, Moazed D. 2004. Budding yeast silencing complexes and regulation of Sir2 activity by protein-protein interactions. Mol. Cell. Biol. 24:6931-46
225. 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 98:415-20
226. Therizols P, Fairhead C, Cabal GG, Genovesio A, Olivo-Marin JC, et al. 2006. Telomere tethering at the nuclear periphery is essential for efficient DNA double strand break repair in subtelomeric region. J. Cell Biol. 172:189-99
227. Thompson JS, Johnson LM, Grunstein M. 1994. Specific repression of the yeast silent mating locus HMR by an adjacent telomere. Mol. Cell. Biol. 14:446-55
228. Thompson JS, Ling X, Grunstein M. 1994. Histone H3 amino terminus is required for telomeric and silent mating locus repression in yeast. Nature 369:245-47
229. Thompson JS, Snow ML, Giles S, McPherson LE, Grunstein M. 2003. Identification of a functional domain within the essential core of histone H3 that is required for telomeric and HM silencing in Saccharomyces cerevisiae. Genetics 163:447-52
230. Tompa R, Madhani HD. 2007. Histone H3 lysine 36 methylation antagonizes silencing in Saccharomyces cerevisiae independently of the Rpd3S histone deacetylase complex. Genetics 175:585-93
231. Tong L, Denu JM. 2010. Function and metabolism of sirtuin metabolite O-acetyl-ADP-ribose. Biochim. Biophys. Acta 1804:1617-25
232. Tornow J, Zeng X, Gao W, Santangelo GM. 1993. GCR1, a transcriptional activator in Saccharomyces cerevisiae, complexes with RAP1 and can function without its DNA binding domain.EMBO J.12:2431-37
233. Triolo T, Sternglanz R. 1996. Role of interactions between the origin recognition complex and SIR1 in transcriptional silencing. Nature 381:251-53
234. Tsukamoto Y, Kato J, Ikeda H. 1997. Silencing factors participate in DNA repair and recombination in Saccharomyces cerevisiae. Nature 388:900-3
235. Tung SY, Hong JY, Walz T, Moazed D, Liou GG. 2012. Chromatin affinity-precipitation using a small metabolic molecule: its application to analysis of O-acetyl-ADP-ribose. Cell Mol. Life Sci. 69:641-50
236. Ugolini S, Bruschi CV. 1996. The red/white colony color assay in the yeast Saccharomyces cerevisiae: epistatic growth advantage of white ade8-18, ade2 cells over red ade2 cells. Curr. Genet. 30:485-92
237. Valenzuela L, Dhillon N, Dubey RN, Gartenberg MR, Kamakaka RT. 2008. Long-range communication between the silencers of HMR. Mol. Cell. Biol. 28:1924-35
238. van Welsem T, Frederiks F, Verzijlbergen KF, Faber AW, Nelson ZW, et al. 2008. Synthetic lethal screens identify gene silencing processes in yeast and implicate the acetylated amino terminus of Sir3 in recognition of the nucleosome core. Mol. Cell. Biol. 28:3861-72
239. Venkatasubrahmanyam S, Hwang WW, Meneghini MD, Tong AH, Madhani HD. 2007. Genome-wide, as opposed to local, antisilencing is mediated redundantly by the euchromatic factors Set1 and H2A.Z. Proc. Natl. Acad. Sci. USA 104:16609-14
240. Verzijlbergen KF, Faber AW, Stulemeijer IJ, van Leeuwen F. 2009. Multiple histone modifications in euchromatin promote heterochromatin formation by redundant mechanisms in Saccharomyces cerevisiae. BMC Mol. Biol. 10:76
241. Viswanathan M, Muthukumar G, Cong YS, Lenard J. 1994. Seripauperins of Saccharomyces cerevisiae: a new multigene family encoding serine-poor relatives of serine-rich proteins. Gene 148:149-53
242. Wang CL, Landry J, Sternglanz R. 2008. A yeast sir2 mutant temperature sensitive for silencing. Genetics 180:1955-62
243. Wang X, Connelly JJ, Wang CL, Sternglanz R. 2004. Importance of the Sir3 N terminus and its acetylation for yeast transcriptional silencing. Genetics 168:547-51
244. Weake VM, Workman JL. 2008. Histone ubiquitination: triggering gene activity. Mol. Cell 29:653-63
245. Weber JM, Ehrenhofer-Murray AE. 2010. Design of a minimal silencer for the silent mating-type locus HML of Saccharomyces cerevisiae. Nucleic Acids Res. 38:7991-8000
246. Weiss K, Simpson RT. 1998. High-resolution structural analysis of chromatin at specific loci: Saccha-romyces cerevisiae silent mating type locus HMLα. Mol. Cell. Biol. 18:5392-403
247. Wotton D, Shore D. 1997. A novel Rap1p-interacting factor, Rif2p, cooperates with Rif1p to regulate telomere length in Saccharomyces cerevisiae. Genes Dev. 11:748-60
248. Xie J, Pierce M, Gailus-Durner V, Wagner M, Winter E, Vershon AK. 1999. Sum1 and Hst1 repress middle sporulation-specific gene expression during mitosis in Saccharomyces cerevisiae. EMBO J. 18:6448-54
249. Xu EY, Zawadzki KA, Broach JR. 2006. Single-cell observations reveal intermediate transcriptional silencing states. Mol. Cell 23:219-29
250. Xu F, Zhang Q, Zhang K, Xie W, Grunstein M. 2007. Sir2 deacetylates histone H3 lysine 56 to regulate telomeric heterochromatin structure in yeast. Mol. Cell 27:890-900
251. Yang B, Britton J, Kirchmaier AL. 2008. Insights into the impact of histone acetylation and methylation on Sir protein recruitment, spreading, and silencing in Saccharomyces cerevisiae. J. Mol. Biol. 381:826-44
252. Yang B, Kirchmaier AL. 2006. Bypassing the catalytic activity of SIR2 for SIR protein spreading in Saccharomyces cerevisiae. Mol. Biol. Cell 17:5287-97
253. Yang B, Miller A, Kirchmaier AL. 2008. HST3/HST4-dependent deacetylation of lysine 56 of histone H3 in silent chromatin. Mol. Biol. Cell 19:4993-5005
254. Yang D, Fang Q, Wang M, Ren R, Wang H, et al. 2013. Nα-acetylated Sir3 stabilizes the conformation of a nucleosome-binding loop in the BAH domain. Nat. Struct. Mol. Biol. 20:116-18
255. Yu MC, Lamming DW, Eskin JA, Sinclair DA, Silver PA. 2006. The role of protein arginine methylation in the formation of silent chromatin. Genes Dev. 20:3249-54
256. Yu Q, Kuzmiak H, Olsen L, Kulkarni A, Fink E, et al. 2010. Saccharomyces cerevisiae Esc2p interacts with Sir2p through a small ubiquitin-like modifier (SUMO)-binding motif and regulates transcriptionally silent chromatin in a locus-dependent manner. J. Biol. Chem. 285:7525-36
257. Zhao K, Chai X, Clements A, Marmorstein R. 2003. Structure and autoregulation of the yeast Hst2 homolog of Sir2. Nat. Struct. Biol. 10:864-71
258. Zill OA, Scannell D, Teytelman L, Rine J. 2010. Co-evolution of transcriptional silencing proteins and the DNA elements specifying their assembly. PLoS Biol. 8:e1000550