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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:Heterochromatin causes epigenetic repression that can be transmitted through multiple cell divisions. However, the mechanisms underlying silencing and stability of heterochromatin are not fully understood. We show that heterochromatin differs from euchromatin in histone turnover and identify histone deacetylase (HDAC) Clr3 as a factor required for inhibiting histone turnover across heterochromatin domains in Schizosaccharomyces pombe. Loss of RNA-interference factors, Clr4 methyltransferase or HP1 proteins involved in HDAC localization causes increased histone turnover across pericentromeric domains. Clr3 also affects histone turnover at the silent mating-type region, where it can be recruited by alternative mechanisms acting in parallel to H3K9me-HP1. Notably, the JmjC-domain protein Epe1 promotes histone exchange, and loss of Epe1 suppresses both histone turnover and defects in heterochromatic silencing. Our results suggest that heterochromatic-silencing factors preclude histone turnover to promote silencing and inheritance of repressive chromatin.

| 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.

2020-01-11 | GSE132797 | GEO

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

Both H4K20 mono-methylation and H3K56 acetylation mark transcription-dependent histone turnover in fission yeast

Project description:Nucleosome dynamics facilitated by histone turnover is required for transcription as well as DNA replication and repair. Histone turnover is often associated with various histone modifications such as H3K56 acetylation (H3K56Ac), H3K36 methylation (H3K36me), and H4K20 methylation (H4K20me). In order to correlate histone modifications and transcription-dependent histone turnover, we performed genome wide analyses for euchromatic regions in G2/M-arrested fission yeast. The results show that transcription-dependent histone turnover at 5’ promoter and 3’ termination regions is directly correlated with the occurrence of H3K56Ac and H4K20 mono-methylation (H4K20me1) in actively transcribed genes. Furthermore, the increase of H3K56Ac and H4K20me1 and antisense RNA production was observed in the absence of the histone H3K36 methyltransferase Set2 and histone deacetylase complex (HDAC) that are involved in the suppression of histone turnover within the coding regions. These results together indicate that H4K20me1 as well as H3K56Ac are bona fide marks for transcription-dependent histone turnover in fission yeast.

2016-06-21 | GSE83538 | GEO

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