Transcriptional silencing in Saccharomyces cerevisiae and Schizosaccharomyces pombe

Nucleic Acids Research

Volumn 30, Issue 7, 2002, Pages 1465-1482

  Huang, Ying ^a  

^a NONE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; DNA; FUNGAL PROTEIN; RIBOSOME DNA; SILENT INFORMATION REGULATOR PROTEIN 2; SWI6 PROTEIN; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; CELL FUNCTION; CELL NUCLEUS; CENTROMERE; CHROMATIN STRUCTURE; CHROMOSOME; CONTROLLED STUDY; DNA REPAIR; EUKARYOTE; GENE INACTIVATION; GENE LOCUS; GENE SILENCING; GENETIC TRANSCRIPTION; INHIBITION KINETICS; MATING TYPE; NONHUMAN; PRIORITY JOURNAL; REGULATORY MECHANISM; REVIEW; SACCHAROMYCES CEREVISIAE; SCHIZOSACCHAROMYCES POMBE; SEQUENCE HOMOLOGY; TELOMERE;

EUKARYOTA; SACCHAROMYCES; SACCHAROMYCES CEREVISIAE; SACCHAROMYCETALES; SCHIZOSACCHAROMYCES; SCHIZOSACCHAROMYCES POMBE;

EID: 0036529517     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/30.7.1465     Document Type: Review

References (272)

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29. Action of a RAP1 carboxy-terminal silencing domain reveals an underlying competition between HMR and telomeres in yeast
30. Role of interactions between the origin recognition complex and SIR1 in transcriptional silencing
31. A histone variant, Htz1p and a Sir1p-like protein, Esc2p, mediate silencing at HMR
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34. Epigenetic inheritance of transcriptional states in Saccharomyces cerevisiae
35. DNA in transcriptionally silent chromatin assumes a distinct topology that is sensitive to cell cycle progression
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37. Identification of a novel allele of SIR3 defective in the maintenance, but not the establishment, of silencing in Saccharomyces cerevisiae
38. The Sir1 protein's association with a silenced chromosome domain
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40. Sum1 and Hst1 repress middle sporulation-specific gene expression during mitosis in Saccharomyces cerevisiae
41. The sum1-1 mutation affects silent mating-type gene transcription in Saccharomyces cerevisiae
42. SUM1-1: A suppressor of silencing defects in Saccharomyces cerevisiae
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44. Conversion of a gene-specific repressor to a regional silencer
45. A novel form of transcriptional silencing by Sum1-1 requires Hst1 and the origin recognition complex
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48. Telomerase and the maintenance of chromosome ends
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58. Telomere position effect in human cells
59. RAP1 and telomere structure regulate telomere position effects in Saccharomyces cerevisiae
60. Silent domains are assembled continuously from the telomere and are defined by promoter distance and strength and by SIR3 dosage
61. Modifiers of position effect are shared between telomeric and silent mating-type loci in Saccharomyces cerevisiae
62. SIR2 and SIR4 interactions differ in core and extended telomeric heterochromatin in yeast
63. A RAP1-interacting protein involved in transcriptional silencing and telomere length regulation
64. A novel Rap1p-interacting factor, Rif2p, cooperates with Rif1p to regulate telomere length in Saccharomyces cerevisiae
65. Rap1p and telomere length regulation in yeast
66. Yeast Ku protein plays a direct role in telomeric silencing and counteracts inhibition by rif proteins
67. Sir proteins, Rif proteins and Cdc13p bind Saccharomyces telomeres in vivo
68. Spreading of transcriptional repressor Sir3 from telomeric heterochromatin
69. Limitations of silencing at native yeast telomeres
70. Protosilencers in Saccharomyces cerevisiae subtelomeric regions
71. Nuclear pore complexes in the organization of silent telomeric chromatin
72. Perinuclear localization of chromatin facilitates transcriptional silencing
73. Components of the Ku-dependent non-homologous end-joining pathway are involved in telomeric length maintenance and telomeric silencing
74. Mutation of yeast Ku genes disrupts the subnuclear organization of telomeres
75. The clustering of telomeres and colocalization with Rap1, Sir3 and Sir4 proteins in wild-type Saccharomyces cerevisiae
76. Localization of Sir2p: The nucleolus as a compartment for silent information regulators
77. Nuclear compartments and gene regulation
78. Localization of yeast telomeres to the nuclear periphery is separable from transcriptional repression and telomere stability functions
79. SIR3 and SIR4 proteins are required for the positioning and integrity of yeast telomeres
80. The nucleolus
81. Transcription in the yeast rRNA gene locus: Distribution of the active gene copies and chromatin structure of their flanking regulatory sequences
82. A new role for a yeast transcriptional silencer gene, SIR2, in regulation of recombination in ribosomal DNA
83. An unusual form of transcriptional silencing in yeast ribosomal DNA
84. Direct evidence for SIR2 modulation of chromatin structure in yeast rDNA
85. Net1, a Sir2-associated nucleolar protein required for rDNA silencing and nucleolar integrity
86. Exit from mitosis is triggered by Tem1-dependent release of the protein phosphatase Cdc14 from nucleolar RENT complex
87. Distribution of a limited Sir2 protein pool regulates the strength of yeast rDNA silencing and is modulated by SIR4p
88. Net1 stimulates RNA polymerase I transcription and regulates nucleolar structure independently of controlling mitotic exit
89. Cfi1 prevents premature exit from mitosis by anchoring Cdc14 phosphatase in the nucleolus
90. Yeast Hct1 is a regulator of Clb2 cyclin proteolysis
91. Cdc20 and Cdh1: A family of substrate-specific activators of apc-dependent proteolysis
92. Cloning and characterization of four SIR genes of Saccharomyces cerevisiae
93. Epigenetic switching of transcriptional states: Cis- and trans-acting factors affecting establishment of silencing at the HMR locus in Saccharomyces cerevisiae
94. Internal tracts of telomeric DNA act as silencers in Saccharomyces cerevisiae
95. Tethered Sir3p nucleates silencing at telomeres and internal loci in Saccharomyces cerevisiae
96. Evidence for silencing compartments within the yeast nucleus: A role for telomere proximity and Sir protein concentration in silencer-mediated repression
97. Silencing of genes at nontelomeric sites in yeast is controlled by sequestration of silencing factors at telomeres by Rap1 protein
98. Functional characterization of the N terminus of Sir3p
99. Mutation in the silencing gene SIR4 can delay aging in Saccharomyces cerevisiae
100. Redistribution of silencing proteins from telomeres to the nucleolus is associated with extension of life span in S. cerevisiae
101. Genetic evidence for an interaction between SIR3 and histone H4 in the repression of the silent mating loci in Saccharomyces cerevisiae
102. Genetic analysis of histone H4: Essential role of lysines subject to reversible acetylation
103. Point mutations in the yeast histone H4 gene prevent silencing of the silent mating type locus HML
104. Histone H3 amino terminus is required for telomeric and silent mating locus repression in yeast
105. Hir proteins are required for position-dependent gene silencing in Saccharomyces cerevisiae in the absence of chromatin assembly factor I
106. Transcriptional silencing of Ty1 elements in the RDN1 locus of yeast
107. A genetic screen for ribosomal DNA silencing defects identifies multiple DNA replication and chromatin-modulating factors
108. Crystal structure of the nucleosome core particle at 2.8 Å resolution
109. Chromatin assembly factor I contributes to the maintenance, but not the re-establishment, of silencing at the yeast silent mating loci
110. The yeast Cac1 protein is required for the stable inheritance of transcriptionally repressed chromatin at telomeres
111. Yeast histone deposition protein Asf1p requires Hir proteins and PCNA for heterochromatic silencing
112. Replication-dependent marking of DNA by PCNA facilitates Caf-1-coupled inheritance of chromatin
113. Ultraviolet radiation sensitivity and reduction of telomeric silencing in Saccharomyces cerevisiae cells lacking chromatin assembly factor-I
114. Postreplicative chromatin assembly by Drosophila and human chromatin assembly factor I
115. Two new S-phase-specific genes from Saccharomyces cerevisiae
116. Identification of high-copy disruptors of telomeric silencing in Saccharomyces cerevisiae
117. The RCAF complex mediates chromatin assembly during DNA replication and repair
118. SET domain proteins modulate chromatin domains in eu- and heterochromatin
119. The set1Δ mutation unveils a novel signaling pathway relayed by the Rad53-dependent hyperphosphorylation of replication protein A that leads to transcriptional activation of repair genes
120. Mammalian homologues of the Polycomb-group gene Enhancer of zeste mediate gene silencing in Drosophila heterochromatin and at Saccharomyces cerevisiae telomeres
121. Interaction between Set1p and checkpoint protein Mec3p in DNA repair and telomere functions
122. The Saccharomyces cerevisiae Set1 complex includes an Ash2 homologue and methylates histone 3 lysine 4
123. Histone acetyltransferases
124. Histone deacetylases: Silencers for hire
125. Roles of histone acetyltransferases and deacetylases in gene regulation
126. Evidence that the transcriptional regulators SIN3 and RPD3 and a novel gene (SDS3) with similar functions, are involved in transcriptional silencing in S. cerevisiae
127. Hda1 and Rpd3 are members of distinct yeast histone deacetylase complexes that regulate silencing and transcription
128. Efficient transcriptional silencing in Saccharomyces cerevisiae requires a heterochromatin histone acetylation pattern
129. A large protein complex containing the yeast Sin3p and Rpd3p transcriptional regulators
130. SAP30, a component of the mSin3 corepressor complex involved in N-CoR-mediated repression by specific transcription factors
131. SAP30, a novel protein conserved between human and yeast, is a component of a histone deacetylase complex
132. Genomewide studies of histone deacetylase function in yeast
133. Sds3 (suppressor of defective silencing 3) is an integral component of the yeast Sin3·Rpd3 histone deacetylase complex and is required for histone deacetylase activity
134. Pho23 is associated with the Rpd3 histone deacetylase and is required for its normal function in regulation of gene expression and silencing in Saccharomyces cerevisiae
135. Yeast Sas silencing genes and human genes associated with AML and HIV-1 Tat interactions are homologous with acetyltransferases
136. The role of Sas2, an acetyltransferase homologue of Saccharomyces cerevisiae, in silencing and ORC function
137. ESA1 is a histone acetyltransferase that is essential for growth in yeast
138. Tip60 acetylates six lysines of a specific class in core histones in vitro
139. GCN5-related histone N-acetyltransferases belong to a diverse superfamily that includes the yeast SPT10 protein
140. Sas3 is a histone acetyltransferase and requires a zinc finger motif
141. The something about silencing protein, Sas3, is the catalytic subunit of NuA3, a yTAF(II)30-containing hat complex that interacts with the Spt16 subunit of the yeast CP (Cdc68/Pob3)-FACT complex
142. Identification of SAS4 and SAS5, two genes that regulate silencing in Saccharomyces cerevisiae
143. SAS4 and SAS5 are locus-specific regulators of silencing in Saccharomyces cerevisiae
144. Transcription factors, normal myeloid development and leukemia
145. The ENL moiety of the childhood leukemia-associated MLL-ENL oncoprotein recruits human Polycomb 3
146. The SIR2 gene family, conserved from bacteria to humans, functions in silencing, cell cycle progression and chromosome stability
147. Phylogenetic classification of prokaryotic and eukaryotic Sir2-like proteins
148. The conserved core of a human SIR2 homologue functions in yeast silencing
149. An enzymatic activity in the yeast Sir2 protein that is essential for gene silencing
150. Characterization of five human cDNAs with homology to the yeast SIR2 gene: SIR2-like proteins (sirtuins) metabolize NAD and may have protein ADP-ribosyltransferase activity
151. Transcriptional silencing and longevity protein Sir2 is an NAD-dependent histone deacetylase
152. Trichostatin A and trapoxin: Novel chemical probes for the role of histone acetylation in chromatin structure and function
153. The silencing protein SIR2 and its homologs are NAD-dependent protein deacetylases
154. +-dependent protein deacetylase activity in the Sir2 protein family
155. Acetylation of TAF(I)68, a subunit of TIF-IB/SL1, activates RNA polymerase I transcription
156. Sir2p exists in two nucleosome-binding complexes with distinct deacetylase activities
157. HST1, a new member of the SIR2 family of genes
158. A cytosolic NAD-dependent deacetylase, Hst2p, can modulate nucleolar and telomeric silencing in yeast
159. SIR2 and aging-the exception that proves the rule
160. Sir2 links chromatin silencing, metabolism and aging
161. Sound silencing: The Sir2 protein and cellular senescence
162. The SIR2/3/4 complex and SIR2 alone promote longevity in Saccharomyces cerevisiae by two different mechanisms
163. Extrachromosomal rDNA circles-a cause of aging in yeast
164. Requirement of NAD and SIR2 for life-span extension by calorie restriction in Saccharomyces cerevisiae
165. An intervention resembling caloric restriction prolongs life span and retards aging in yeast
166. Silencing factors participate in DNA repair and recombination in Saccharomyces cerevisiae
167. Relocalization of telomeric Ku and SIR proteins in response to DNA strand breaks in yeast
168. DNA damage triggers disruption of telomeric silencing and Mec1p-dependent relocation of Sir3p
169. MEC1-dependent redistribution of the Sir3 silencing protein from telomeres to DNA double-strand breaks
170. Checkpoint proteins influence telomeric silencing and length maintenance in budding yeast
171. Role of yeast SIR genes and mating type in directing DNA double-strand breaks to homologous and non-homologous repair paths
172. Yeast cell-type regulation of DNA repair
173. a/α-control of DNA repair in the yeast Saccharomyces cerevisiae: Genetic and physiological aspects
174. Suppression of a new allele of the yeast RAD52 gene by overexpression of RAD51, mutations in srs2 and ccr4, or mating-type heterozygosity
175. Expression of Saccharomyces cerevisiae MATa and MATa enhances the HO endonuclease-stimulation of chromosomal rearrangements directed by his3 recombinational substrates
176. Zip1 is a synaptonemal complex protein required for meiotic chromosome synapsis
177. Role for the silencing protein Dot1 in meiotic checkpoint control
178. Pch2 links chromatin silencing to meiotic checkpoint control
179. Chromatin silencing protein and pachytene checkpoint regulator Dot1p has a methyltransferase fold
180. Rearrangements of the transposable mating-type cassettes of fission yeast
181. Mating-type switching and mitotic crossing-over at the mating-type locus in fission yeast
182. A recombinationally repressed region between mat2 and mat3 loci shares homology to centromeric repeats and regulates directionality of mating-type switching in fission yeast
183. Three additional linkage groups that repress transcription and meiotic recombination in the mating-type region of Schizosaccharomyces pombe
184. Initiation of meiotic recombination by double-strand DNA breaks in Schizosaccharomyces pombe
185. Unblocking of meiotic crossing-over between the silent mating-type cassettes of fission yeast, conditioned by the recessive, pleotropic mutant rik1
186. Chromosomal inheritance of epigenetic states in fission yeast during mitosis and meiosis
187. Epigenetic inheritance of transcriptional silencing and switching competence in fission yeast
188. Repression of a mating type cassette in the fission yeast by four DNA elements
189. Localization and properties of a silencing element near the mat3-M mating-type cassette of Schizosaccharomyces pombe
190. Position effect variegation at the mating-type locus of fission yeast: A cis-acting element inhibits covariegated expression of genes in the silent and expressed domains
191. A fission yeast repression element cooperates with centromere-like sequences and defines a mat silent domain boundary
192. Transitions in distinct histone H3 methylation patterns at the heterochromatin domain boundaries
193. + disrupt the localisation of the chromo domain protein Swi6p and impair centromere function
194. The chromodomain protein Swi6: A key component at fission yeast centromeres
195. The clr1 locus regulates the expression of the cryptic mating-type loci of fission yeast
196. Histone deacetylase homologs regulate epigenetic inheritance of transcriptional silencing and chromosome segregation in fission yeast
197. Mutations in rik1, clr2, clr3 and clr4 genes asymmetrically derepress the silent mating-type loci in fission yeast
198. Role of histone H3 lysine 9 methylation in epigenetic control of heterochromatin assembly
199. Regulation of chromatin structure by site-specific histone H3 methyltransferases
200. The chromo superfamily: New members, duplication of the chromo domain and possible role in delivering transcription regulators to chromatin
201. Chromo-domain proteins: Linking chromatin structure to epigenetic regulation
202. The chromo and SET domains of the Clr4 protein are essential for silencing in fission yeast
203. Isolation and characterization of Suv39h2, a second histone H3 methyltransferase gene that displays testis-specific expression
204. Re-SET-ting heterochromatin by histone methyltransferases
205. Methylation of histone H3 lysine 9 creates a binding site for HP1 proteins
206. The chromo shadow domain, a second chromo domain in heterochromatin-binding protein 1, HP1
207. Switching gene swi6, involved in repression of silent mating-type loci in fission yeast, encodes a homologue of chromatin-associated proteins from drosophila and mammals
208. The polycomb protein shares a homologous domain with a heterochromatin-associated protein of drosophila
209. A chromodomain protein, Swi6, performs imprinting functions in fission yeast during mitosis and meiosis
210. A deubiquitinating enzyme interacts with SIR4 and regulates silencing in Saccharomyces cerevisiae
211. PSI-BLAST searches using hidden markov models of structural repeats: Prediction of an unusual sliding DNA clamp and of β-propellers in UV-damaged DNA-binding protein
212. Nucleosome assembly by a complex of CAF-1 and acetylated histones H3/H4
213. + is required for chromosome segregation and shows a genetic interaction with α-tubulin
214. Four chromo-domain proteins of Schizosaccharomyces pombe differentially repress transcription at various chromosomal locations
215. +, a putative fission yeast histone deacetylase gene
216. +, a histone deacetylase gene of Schizosaccharomyces pombe, is required for the meiotic cell cycle and resistance to trichostatin a
217. A low copy number central sequence with strict symmetry and unusual chromatin structure in fission yeast centromere
218. Distinct protein interaction domains and protein spreading in a complex centromere
219. Fission yeast mutants that alleviate transcriptional silencing in centromeric flanking repeats and disrupt chromosome segregation
220. Defects in components of the proteasome enhance transcriptional silencing at fission yeast centromeres and impair chromosome segregation
221. Histone acetylation and an epigenetic code
222. The language of covalent histone modifications
223. High resolution cosmid and P1 maps spanning the 14 MB genome of the fission yeast Schizosaccharomyces pombe
224. The 5.8S RNA gene sequence and the ribosomal repeat of Schizosaccharomyces pombe
225. Identification of human Rap1: Implications for telomere evolution
226. Identification of fission yeast nuclear markers using random polypeptide fusions with green fluorescent protein
227. Defective meiosis in telomere-silencing mutants of Schizosaccharomyces pombe
228. Two modes of survival of fission yeast without telomerase
229. + gene is a SIR2 homologue with silencing and centromeric functions
230. The ubiquitin-conjugating enzyme Rad6 (Ubc2) is required for silencing in Saccharomyces cerevisiae
231. Yeast RAD6 encoded ubiquitin conjugating enzyme mediates protein degradation dependent on the n-end-recognizing e3 enzyme
232. Mutation of cysteine-88 in the Saccharomyces cerevisiae Rad6 protein abolishes its ubiquitin-conjugating activity and its various biological functions
233. Characterization of novel rad6/ubc2 ubiquitin-conjugating enzyme mutants in yeast
234. A novel function of the DNA repair gene rhp6 in mating-type silencing by chromatin remodeling in fission yeast
235. DNA end-joining: From yeast to man
236. Yeast Ku as a regulator of chromosomal DNA end structure
237. The yeast Ku heterodimer is essential for protection of the telomere against nucleolytic and recombinational activities
238. Telomere maintenance is dependent on activities required for end repair of double-strand breaks
239. Novel functional requirements for non-homologous DNA end joining in Schizosaccharomyces pombe
240. Protein kinase activity of Tel1p and Mec1p, two Saccharomyces cerevisiae proteins related to the human atm protein kinase
241. Involvement of the checkpoint protein Mec1p in silencing of gene expression at telomeres in Saccharomyces cerevisiae
242. The Saccharomyces cerevisiae suppressor of choline sensitivity (SCS2) gene is a multicopy suppressor of mec1 telomeric silencing defects
243. The ribonucleotide reductase inhibitor Sml1 is a new target of the Mec1/Rad53 kinase cascade during growth and in response to DNA damage
244. The Saccharomyces cerevisiae SCS2 gene product, a homolog of a synaptobrevin-associated protein, is an integral membrane protein of the endoplasmic reticulum and is required for inositol metabolism
245. +
246. Asf1 links Rad53 to control of chromatin assembly
247. Dynamic interaction of DNA damage checkpoint protein Rad53 with chromatin assembly factor asf1
248. A region of the Sir1 protein dedicated to recognition of a silencer and required for interaction with the Orc1 protein in Saccharomyces cerevisiae
249. The function of DNA polymerase α at telomeric g tails is important for telomere homeostasis
250. Proliferating cell nuclear antigen is required for DNA excision repair
251. Pcna connects DNA replication to epigenetic inheritance in yeast
252. DNA repair synthesis during base excision repair in vitro is catalyzed by DNA polymerase ε and is influenced by DNA polymerases α and δ in Saccharomyces cerevisiae
253. A role for the replication proteins PCNA, RF-C, polymerase ε and Cdc45 in transcriptional silencing in Saccharomyces cerevisiae
254. The origin recognition complex, Sir1 and the S phase requirement for silencing
255. Separable functions of Orc5 in replication initiation and silencing in Saccharomyces cerevisiae
256. The origin recognition complex has essential functions in transcriptional silencing and chromosomal replication
257. DNA replication-independent silencing in Saccharomyces cerevisiae
258. Establishment of transcriptional silencing in the absence of DNA replication
259. A role for DNA polymerase α in epigenetic control of transcriptional silencing in fission yeast
260. Chromodomain protein Swi6-mediated role of DNA polymerase α in establishment of silencing in fission yeast
261. Lineage-specific loss and divergence of functionally linked genes in eukaryotes
262. Active genes in budding yeast display enhanced in vivo accessibility to foreign DNA methylases: A novel in vivo probe for chromatin structure of yeast
263. Telomeric chromatin modulates replication timing near chromosome ends
264. The ORC1 homolog orp1 in fission yeast plays a key role in regulating onset of S phase
265. Sum1, a highly conserved WD-repeat protein, suppresses S-M checkpoint mutants and inhibits the osmotic stress cell cycle response in fission yeast
266. A new member of the Sin3 family of corepressors is essential for cell viability and required for retroelement propagation in fission yeast
267. Three yeast proteins related to the human candidate tumor suppressor p33(ING1) are associated with histone acetyltransferase activities
268. Characterization of Schizosaccharomyces pombe Hus1: A PCNA-related protein that associates with Rad1 and Rad9
269. Fission yeast Chk1 protein kinase links the rad checkpoint pathway to cdc2
270. Isolation and analysis of the fission yeast gene encoding polymerase delta accessory protein PCNA
271. Fission yeast Cdc24 is a replication factor C- and proliferating cell nuclear antigen-interacting factor essential for S-phase completion
272. + encodes DNA polymerase ε and is required for chromosomal replication but not for the S phase checkpoint