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A trithorax-group complex purified from Saccharomyces cerevisiae is required for methylation of histone H3
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Methylation of histone H3 at lysine 4 is highly conserved and correlates with transcriptionally active nuclei in Tetrahymena
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Methylation of histone H3 Lys 4 in coding regions of active genes
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While Set1p and H3-K4 methylation have been linked to silencing in yeast, genome-wide analysis of histone methylation and acetylation patterns by chromatin immunoprecipitation shows that H3-K4 methylation correlates with transcriptional activity. The modification is enriched in coding regions. Telomeres and silent mating type loci are hypomethylated. These findings suggest that Set1p and H3-K4 methylation affect silencing indirectly.
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Bernstein B.E., Humphrey E.L., Erlich R.L., Schneider R., Bouman P., Liu J.S., Kouzarides T., Schreiber S.L. Methylation of histone H3 Lys 4 in coding regions of active genes. Proc Natl Acad Sci USA. 11:2002;11. While Set1p and H3-K4 methylation have been linked to silencing in yeast, genome-wide analysis of histone methylation and acetylation patterns by chromatin immunoprecipitation shows that H3-K4 methylation correlates with transcriptional activity. The modification is enriched in coding regions. Telomeres and silent mating type loci are hypomethylated. These findings suggest that Set1p and H3-K4 methylation affect silencing indirectly.
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Proc Natl Acad Sci USA
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Boggs B.A., Cheung P., Heard E., Spector D.L., Chinault A.C., Allis C.D. Differentially methylated forms of histone H3 show unique association patterns with inactive human X chromosomes. Nat Genet. 30:2002;73-76.
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Narlikar G.J., Fan H.Y., Kingston R.E. Cooperation between complexes that regulate chromatin structure and transcription. Cell. 108:2002;475-487.
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Marmorstein R. Protein modules that manipulate histone tails for chromatin regulation. Nat Rev Mol Cell Biol. 2:2001;422-432.
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Microarray deacetylation maps determine genome-wide functions for yeast histone deacetylases
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Genomewide histone acetylation maps reveal the in vivo target genes and target histone sites of all the histone deacetylases in yeast. The datasets suggest that acetylation of histone H4-K5 and H4-K12 correlates with increased transcription in the rpd3Δ strain. Acetylation of histone H4-K16 is much less affected, indicating that it may not be directly involved in transcriptional regulation. This study identified subtelomeric regions, called HAST domains, that are deacetylated and repressed by Hda1p.
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Robyr D., Suka Y., Xenarios I., Kurdistani S.K., Wang A., Suka N., Grunstein M. Microarray deacetylation maps determine genome-wide functions for yeast histone deacetylases. Cell. 109:2002;437-446. Genomewide histone acetylation maps reveal the in vivo target genes and target histone sites of all the histone deacetylases in yeast. The datasets suggest that acetylation of histone H4-K5 and H4-K12 correlates with increased transcription in the rpd3Δ strain. Acetylation of histone H4-K16 is much less affected, indicating that it may not be directly involved in transcriptional regulation. This study identified subtelomeric regions, called HAST domains, that are deacetylated and repressed by Hda1p.
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The silencing complex SAS-I links histone acetylation to the assembly of repressed chromatin by CAF-I and Asf1 in Saccharomyces cerevisiae
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This study, together with Osada et al. (2001) [54•], shows that the putative acetyltransferase, Sas2p, is found in a nuclear protein complex with the chromatin assembly factors Cac1p and Asf1p. Deletion of any of these genes weakens silencing in yeast, as does mutation of H4-K16 to arginine, suggesting that Sas2p acts through acetylation of H4-K16, possibly in coordination with chromatin assembly.
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Meijsing S.H., Ehrenhofer-Murray A.E. The silencing complex SAS-I links histone acetylation to the assembly of repressed chromatin by CAF-I and Asf1 in Saccharomyces cerevisiae. Genes Dev. 15:2001;3169-3182. This study, together with Osada et al. (2001) [54•], shows that the putative acetyltransferase, Sas2p, is found in a nuclear protein complex with the chromatin assembly factors Cac1p and Asf1p. Deletion of any of these genes weakens silencing in yeast, as does mutation of H4-K16 to arginine, suggesting that Sas2p acts through acetylation of H4-K16, possibly in coordination with chromatin assembly.
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Genes Dev
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Meijsing, S.H.1
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54
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The yeast SAS (something about silencing) protein complex contains a MYST-type putative acetyltransferase and functions with chromatin assembly factor ASF1
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See annotation Meijsing et al. (2001) [53•].
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Osada S., Sutton A., Muster N., Brown C.E., Yates J.R. iii, Sternglanz R., Workman J.L. The yeast SAS (something about silencing) protein complex contains a MYST-type putative acetyltransferase and functions with chromatin assembly factor ASF1. Genes Dev. 15:2001;3155-3168. See annotation Meijsing et al. (2001) [53•].
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Katan-Khaykovich Y., Struhl K. Dynamics of global histone acetylation and deacetylation in vivo: rapid restoration of normal histone acetylation status upon removal of activators and repressors. Genes Dev. 16:2002;743-752.
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0034934774
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Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association
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Using chromatin immunoprecipitation, this study shows that Rap1p binds to 5% of all the yeast genes. Rap1p binds the most heavily transcribed genes and predominantly in intergenic regions. One hundred and eighty five new binding sites are found. Sir2, Sir3 and Sir4 protein binding was mapped at a genome-wide scale and found at silent loci, but also at multiple nonsilenced loci, the significance of which remains unclear. Some of the new Sir binding sites co-localize with Rap1p and/or origin of replication complex binding sites.
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Lieb J.D., Liu X.L., Botstein D., Brown P.O. Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association. Nat Genet. 28:2001;327-334. Using chromatin immunoprecipitation, this study shows that Rap1p binds to 5% of all the yeast genes. Rap1p binds the most heavily transcribed genes and predominantly in intergenic regions. One hundred and eighty five new binding sites are found. Sir2, Sir3 and Sir4 protein binding was mapped at a genome-wide scale and found at silent loci, but also at multiple nonsilenced loci, the significance of which remains unclear. Some of the new Sir binding sites co-localize with Rap1p and/or origin of replication complex binding sites.
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Nat Genet
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Lieb, J.D.1
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59
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Genome-wide distribution of ORC and MCM proteins in S. cerevisiae: High-resolution mapping of replication origins
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This study identifies binding sites for origin of replication complex (ORC) and mini-chromosome maintenance (MCM) proteins in the yeast genome by chromatin immunoprecipitation. Origins of replication were predicted based on co-localization of MCM or ORC proteins, or both. The yeast genome is estimated to contain ∼400 origins of replication.
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Wyrick J.J., Aparicio J.G., Chen T., Barnett J.D., Jennings E.G., Young R.A., Bell S.P., Aparicio O.M. Genome-wide distribution of ORC and MCM proteins in S. cerevisiae: high-resolution mapping of replication origins. Science. 294:2001;2357-2360. This study identifies binding sites for origin of replication complex (ORC) and mini-chromosome maintenance (MCM) proteins in the yeast genome by chromatin immunoprecipitation. Origins of replication were predicted based on co-localization of MCM or ORC proteins, or both. The yeast genome is estimated to contain ∼400 origins of replication.
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Science
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Wyrick, J.J.1
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60
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Histone H3 lysine 4 methylation disrupts binding of nucleosome remodeling and deacetylase (NuRD) repressor complex
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Zegerman P., Canas B., Pappin D., Kouzarides T. Histone H3 lysine 4 methylation disrupts binding of nucleosome remodeling and deacetylase (NuRD) repressor complex. J Biol Chem. 277:2002;11621-11624.
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Regulation of the different chromatin states of autosomes and X chromosomes in the germ line of C. elegans
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Maternaleffect sterile proteins MES-2, MES-3, MES-4 and MES6 are required to keep the X chromosomes in a repressed state in the C. elegans germ line. Immunolocalization studies reveal that MES-4 is restricted to autosomes. The (repressor) complex MES-2-MES-3-MES6 is required to exclude MES-4 from X chromosomes. MES-4, in turn, may provide specificity of silencing by excluding the MES-2-MES-3-MES6 complex and other repressors from the autosomes, thereby targeting the repressors to the X-chromosomes.
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Fong Y., Bender L., Wang W., Strome S. Regulation of the different chromatin states of autosomes and X chromosomes in the germ line of C. elegans. Science. 296:2002;2235-2238. Maternaleffect sterile proteins MES-2, MES-3, MES-4 and MES6 are required to keep the X chromosomes in a repressed state in the C. elegans germ line. Immunolocalization studies reveal that MES-4 is restricted to autosomes. The (repressor) complex MES-2-MES-3-MES6 is required to exclude MES-4 from X chromosomes. MES-4, in turn, may provide specificity of silencing by excluding the MES-2-MES-3-MES6 complex and other repressors from the autosomes, thereby targeting the repressors to the X-chromosomes.
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Science
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Fong, Y.1
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62
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Active genes are tri-methylated at K4 of histone H3
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This paper demonstrates that histone H3-K4 dimethylation occurs both in active and inactive euchromatic genes but that trimethylation is an exclusive mark of active genes. The authors confirm that Set1p is the enzyme responsible for both forms of methylation in vivo and in vitro. SET1 is required for maximal expression of a large number of euchromatic genes. The authors suggest that dimethylated Lys4 keeps chromatin in a transcriptionally permissive state and that trimethylated Lys4 is important for a transcriptionally active chromatin conformation.
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Santos-Rosa H., Schneider R., Bannister A.J., Sherriff J., Bernstein B.E., Emre N.C., Schreiber S.L., Mellor J., Kouzarides T. Active genes are tri-methylated at K4 of histone H3. Nature. 419:2002;407-411. This paper demonstrates that histone H3-K4 dimethylation occurs both in active and inactive euchromatic genes but that trimethylation is an exclusive mark of active genes. The authors confirm that Set1p is the enzyme responsible for both forms of methylation in vivo and in vitro. SET1 is required for maximal expression of a large number of euchromatic genes. The authors suggest that dimethylated Lys4 keeps chromatin in a transcriptionally permissive state and that trimethylated Lys4 is important for a transcriptionally active chromatin conformation.
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(2002)
Nature
, vol.419
, pp. 407-411
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Santos-Rosa, H.1
Schneider, R.2
Bannister, A.J.3
Sherriff, J.4
Bernstein, B.E.5
Emre, N.C.6
Schreiber, S.L.7
Mellor, J.8
Kouzarides, T.9
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