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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Asf1/HIRA facilitate global histone deacetylation and associate with HP1 to promote nucleosome occupancy at heterochromatic loci (expression)

ABSTRACT: Expression profile of Schizosaccharomyces pombe genome in asf1-1 and ∆hip1 cells. Expression profile of mutant cells compared to wild-type cells. Agilent 60mer oligonucleotide custom array containing probes spanning large portion of chromosome 2 at 50bp resolution was used to profile expression levels in mutant cells and to compare them to levels in wild-type cells.

ORGANISM(S): Schizosaccharomyces pombe

SUBMITTER: Kenichi Yamane

PROVIDER: E-GEOD-25598 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Asf1/HIRA facilitate global histone deacetylation and associate with HP1 to promote nucleosome occupancy at heterochromatic loci

Project description:This SuperSeries is composed of the following subset Series: GSE25597: Asf1/HIRA facilitate global histone deacetylation and associate with HP1 to promote nucleosome occupancy at heterochromatic loci (ChIP-chip) GSE25598: Asf1/HIRA facilitate global histone deacetylation and associate with HP1 to promote nucleosome occupancy at heterochromatic loci (expression) GSE25600: Asf1/HIRA facilitate global histone deacetylation and associate with HP1 to promote nucleosome occupancy at heterochromatic loci (MNase) Refer to individual Series

2011-01-07 | E-GEOD-25605 | biostudies-arrayexpress

Asf1/HIRA facilitate global histone deacetylation and associate with HP1 to promote nucleosome occupancy at heterochromatic loci (expression)

Project description:Expression profile of Schizosaccharomyces pombe genome in asf1-1 and ∆hip1 cells. Expression profile of mutant cells compared to wild-type cells.

2011-01-07 | GSE25598 | GEO

Clr4/Suv39 and RNA quality control factors cooperate to trigger RNAi and suppress antisense RNA (expression)

Project description:Expression profile of Schizosaccharomyces pombe genome in ?mlo3, mlo3-A, mlo3-A?h2a.z, ?cid14?h2a.z and mlo3-A?cid14 cells. Expression profile of mutant cells compared to wild-type cells. Agilent 60mer oligonucleotide custom array containing probes spanning large portion of chromosome 2 at 50bp resolution was used to profile expression levels in mutant cells and to compare them to levels in wild-type cells.

2011-04-12 | E-GEOD-26995 | biostudies-arrayexpress

High resolution Hi-C analysis in S. pombe reveals fundamental elements of genome architecture [Expression Array]

Project description:Eukaryotic genomes are folded into three-dimensional structures that govern diverse hromosomal procsses. Studeis in Drosophila and mammals have revealed large self-associating tomological domains whose borders are enriched in cohesin/CTCF factors that are required for long-range intrations. However, mechanisms governing higher-order folding of chromatin fivbers and the exact function of cohesin in this process remain poor understood. Here we perform Hi-C to explore the organization of the Schizosaccharomyces pombe genome at high-resolution, which despite its small size comprises fundamental features found in higher eukaryotes. Our analyses reveal that in addition to determinants of Rabl-like chromosome architecture, smaller locally interacting regions of chromatin, referred to as globules, are a distinctive features of S. pombe chromosome organization. This feature of chromatin architecture requires a function of cohesin distinct from its role in sister chromatid cohesion. Cohesin is enriched at globule boundaries and its loss causes disruption of local globule structure and global chromosome territories. Heterochromatin, which selectively loads cohesin at specific loci including pericentromric and subtelomeric domains, is dispensable for globule formation but uniquely impacts genome organization through chromatin compaction by enforcing Rabl configuration. Agilent 60mer oligonucleotide custom array containing probes spanning large portion of chromosome 2 at 50bp resolution was used to profile expression levels in mutant cells and to compare them to levels in wild type cells.

2014-10-22 | E-GEOD-57159 | biostudies-arrayexpress

Histone H4 acetylation in wild-type, ASF1, SET2 and ASF1 SET2 deletion yeast strains

Project description:ChIP-on chip assays to measure the change in histone acetylation over the yeast genome, in ASF1, SET2 and ASF1 SET2 deletion yeast strains compared to the wild-type control. ChIPs of AcH4 from wild-type, ASF1, SET2 and ASF1 SET2 deletion yeast strains were normalized to the H3 enrichment.

2012-07-25 | GSE28098 | GEO

Histone H2A.Z cooperates with RNAi and heterochromatin factors to suppress antisense RNAs

Project description:Expression profile of mutant cells compared to wild-type cells: Expression profile of Schizosaccharomyces pombe genome in ∆pht1, ∆ago1, ∆clr4, rik1, ∆pht1rik1, ∆pht1∆ago1 and ∆pht1∆clr4 cells. Expression profile of Schizosaccharomyces pombe genome in ∆rrp6, ∆cid14, ∆swi6, ∆swr1, ∆set1, ∆pht1∆swi6 and ∆pht1∆set1 cells. Expression profile of Schizosaccharomyces pombe genome in ∆alp13, ∆cph1, ∆set2, clr6-1 and ∆cph1∆pht1 cells. Occupancy profiling: Occupancy profiling of RNA polymerase II, histone variant H2A.Z and ClrC subunit Rik1 in fission yeast Schizosaccharomyces pombe Occupancy profiling of histone variant H2A.Z in ∆msc1 cells. Agilent 60mer oligonucleotide custom array containing probes spanning large portion of chromosome 2 at 50bp resolution was used to profile expression levels in mutant cells and to compare them to levels in wild-type cells. Agilent 60mer array was used to analyze DNA recovered by immunoprecipitation of RNA polymerase II, H2A.Z or Rik1 from asynchronous culture of fission yeast. Agilent 60mer array was used to analyze DNA recovered by immunoprecipitation of histone H2A.Z from asynchronous culture of fission yeast.

2009-08-25 | E-GEOD-17271 | biostudies-arrayexpress

ASF1

Project description:Transcription profiling by array of HeLa cells after the knock-down of ASF1 (ASF1a & ASF1b) by siRNA compared to non-targeting control siRNA

2014-01-14 | E-MTAB-1909 | biostudies-arrayexpress

Asf1/HIRA facilitate global histone deacetylation and associate with HP1 to promote nucleosome occupancy at heterochromatic loci.

Project description: Not available

| S-EPMC3035992 | biostudies-literature

Histone chaperone ASF1 mediates H3.3-H4 deposition in Arabidopsis

Project description:Histone chaperones and chromatin remodelers control nucleosome dynamics, which are essential for transcription, replication, and DNA repair. The histone chaperone Anti-Silencing Factor 1 (ASF1) plays a central role in facilitating CAF-1-mediated replication-dependent H3.1 deposition and HIRA-mediated replication-independent H3.3 deposition in yeast and metazoans. Whether ASF1 function is evolutionarily conserved in plants is unknown. Here, we show that Arabidopsis ASF1 proteins display a preference for the HIRA complex. Simultaneous mutation of both Arabidopsis ASF1 genes caused a decrease in chromatin density and ectopic H3.1 occupancy at loci typically enriched with H3.3. Genetic, transcriptomic, and proteomic data indicate that ASF1 proteins strongly prefers the HIRA complex over CAF-1. asf1 mutants also displayed an increase in spurious Pol II transcriptional initiation and showed defects in the maintenance of gene body CG DNA methylation and in the distribution of histone modifications. Furthermore, ectopic targeting of ASF1 caused excessive histone deposition, less accessible chromatin, and gene silencing. These findings reveal the importance of ASF1-mediated histone deposition for proper epigenetic regulation of the genome.

2022-10-27 | GSE188493 | GEO

Cellular quiescence is dependent upon the HIRA histone chaperone

Project description:Quiescence (G0) is a reversible non-dividing state that facilitates cellular survival in adverse conditions. Here we demonstrate that the function of the HIRA histone chaperone complex is required for viability during nitrogen-starvation induced quiescence in Schizosaccharomyces pombe. G0 cells lacking the HIRA protein, Hip1 exhibit elevated levels of antisense ncRNAs and an increase in unrepaired DNA double strand breaks. Nitrogen-starved hip1∆ cells retain metabolic activity but, in contrast to wild type, rapidly lose the ability to resume proliferation. After a short period in G0 (1 day), hip1∆ mutants are able to resume cell growth in response to the restoration of a nitrogen source, but do not efficiently induce Start-specific gene expression and re-enter the cell cycle. However, hip1∆ cells rapidly progress to an unresponsive state and by 4 days in G0, the majority no longer initiate growth following nitrogen source restoration. Analysis using a conditional hip1 allele is consistent with these findings and indicates that HIRA is required for efficient exit from quiescence and prevents a permanent cell cycle arrest.

2023-11-13 | GSE129599 | GEO

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