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HDAC mediated suppression of histone turnover promotes epigenetic stability of heterochromatin

ABSTRACT: Analysis of histone H3 turnover in wild-type and mutant fission yeast cells by using MNase-ChIP-chip

ORGANISM(S): Schizosaccharomyces pombe

PROVIDER: GSE45378 | GEO | 2013/04/21

SECONDARY ACCESSION(S): PRJNA193687

REPOSITORIES: GEO

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HDAC mediated suppression of histone turnover promotes epigenetic stability of heterochromatin

Project description:Analysis of histone H3 turnover in wild-type and mutant fission yeast cells by using MNase-ChIP-chip Exponentially growing cultures of fission yeast cells expressing an ectopic copy of FLAG tagged histone H3 under the control of inv1 promoter were synchronized and expression of H3-FLAG was induced by changing the carbon source of the medium to Sucrose. Cells were crosslinked with 1% Formaldehyde and chromatin was fragmented into mononucleosomes by using micrococcal nuclease (MNase). Chromatin immunoprecipitated DNA recovered with anti-FLAG antibody from wild-type and mutant fission yeast cells and whole cell extracts DNA were amplified by random priming and respectively labeled with Cy5 and Cy3. Labeled DNA samples were mixed and hybridized onto 44k pombe Agilent oligo arrays. Data were processed using Agilent scanner and Feature Extraction software.

2013-04-21 | E-GEOD-45378 | biostudies-arrayexpress

HDAC-mediated suppression of histone turnover promotes epigenetic stability of heterochromatin.

Project description: Not available

| S-EPMC3661211 | biostudies-literature

Nuclear peripheral positioning of heterochromatin by Amo1NUPL2 suppresses nucleosome turnover to promote epigenetic inheritance [ChIP-chip_C300]

Project description:Occupancy profiling of GFP-tagged Rix1, Las1, Ipi1, Crb3 proteins in fission yeast. Occupancy profiling of lysine 9 trimethylated histone H3 in fission yeast.

2020-01-11 | GSE132862 | GEO

Nuclear peripheral positioning of heterochromatin by Amo1NUPL2 suppresses nucleosome turnover to promote epigenetic inheritance [ChIP-chip_C50]

Project description:Occupancy profiling of FLAG-tagged H3 in fission yeast.

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Histone turnover during DNA replication

Project description:Using a recently established histone turnover sensor, we measured the genome-wide H3 turnover during S-phase in S.cerevisiae.

2022-02-18 | GSE193044 | GEO

The histone chaperone FACT facilitates heterochromatin spreading through regulation of histone turnover and H3K9 methylation states

Project description:Heterochromatin formation requires several steps involving: nucleation followed by spreading of large, silent domains and its faithful re-establishment and maintenance after each replication cycle. The essential histone chaperone FACT has been implicated in heterochromatin silencing, however, little is known about the specificity of FACT in this process. Here, by applying single cell assays, ChIP and genetics, we show that FACT mutants have defects in the spreading of heterochromatin at subtelomeres and mating type locus in fission yeast. Further, we demonstrate that the transition of H3K9me2 to me3 is impaired in the FACT mutant and we link the spreading function of FACT to its role in histone turnover suppression. We also identify Epe1 as a specific factor that counteracts heterochromatin spreading defects in the FACT mutants. Together, our studies identify FACT as a first histone chaperone that promotes heterochromatin spreading and add to the current models on histone turnover in propagation of epigenetic marks.

2021-10-12 | GSE174641 | GEO

RNA elimination machinery targeting meiotic mRNAs promotes facultative heterochromatin formation

Project description:Occupancy profiling of lysine 9 dimethylated histone H3 in fission yeast. Agilent 60mer array was used to analyze DNA recovered by immunoprecipitation of lysine 9 dimethylated histone H3 from asynchronous culture of fission yeast.

2011-12-01 | E-GEOD-33404 | biostudies-arrayexpress

A nucleosome turnover map reveals that the stability of histone H4 Lys20 methylation depend on histone recycling in transcribed chromatin [ChIP]

Project description:Nucleosome composition actively contribute to the chromatin structure and accessibility. To preserve chromatin state during replication, transcription and DNA repair, cells have evolved mechanisms to evict or recycle histones, generating a landscape of differentially aged nucleosomes. To map the stability of nucleosomes, we have adapted the recombination induced tag exchange (RITE) method to Schizosaccharomyces pombe histone H3. The RITE method allows us to study replication-independent protein turnover both through the occurrence of, in our case, new histone H3 and the disappearance or preservation of old histone H3. We contrast the RITE system to nucleosome turnover measured by chromatin incorporation of an epitope-tagged H3 under an inducible promoter. We confirm previous findings that stable nucleosomes are found at heterochromatin, but also at coding regions of actively transcribed genes. Genome-wide comparisons with several chromatin marks showed that high turnover nucleosomes correlate with H2A.Z, acetylated H4 and H3K4me2. The histones with high turnover are primarily found at the nucleosomes on the 5´and/or 3´ edges of the transcribed unit. In addition, in this study we have determined genome-wide maps of all three methylation marks at H4K20. All methylation of H4K20 appeared in low turnover nucleosomes and particularly in euchromatic regions. H4K20me1 marks stable nucleosomes at loci proximal to nucleosome depleted regions (NDR) and H4K20me2/3 were found further inside of transcribed units, especially at coding regions of long genes expressed at low levels. Further, this transcription-dependent accumulation of histone methylations was dependent on the histone chaperone complex FACT (Facilitates Chromatin Transcription), as predicited from its role in recycling nucleosomes during transcription.

2015-03-06 | GSE59461 | GEO

A nucleosome turnover map reveals that the stability of histone H4 Lys20 methylation depend on histone recycling in transcribed chromatin [ChIP-exo]

2015-03-13 | GSE66865 | GEO

A conserved factor Dhp1/Rat1/Xrn2 triggers premature transcription termination and nucleates heterochromatin to promote gene silencing [ChIP-chip]

Project description:Occupancy profiling of lysine 9 dimethylated histone H3 in fission yeast. Occupancy profiling of Red1, Mtl1, and Mmi1 proteins in fission yeast. Agilent 60mer array was used to analyze DNA recovered by immunoprecipitation of lysine 9 dimethylated histone H3, Red1, Mtl1, and Mmi1 proteins from asynchronous culture of fission yeast.

2016-01-05 | E-GEOD-74740 | biostudies-arrayexpress

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