Hrp3 controls nucleosome positioning to suppress non-coding transcription in eu- and heterochromatin [MNase-Seq]
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ABSTRACT:
ORGANISM(S): Schizosaccharomyces pombe
PROVIDER: GSE40451 | GEO | 2012/10/02
SECONDARY ACCESSION(S): PRJNA174085
REPOSITORIES: GEO
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Project description:We report that the Schizosaccharomyces pombe CHD remodeler, Hrp3, is a global regulator that drives higher-order chromatin structure and genomic stability. The loss of Hrp3 resulted in nucleosome perturbation across the chromosome, and the production of antisense transcripts in the hrp3M-bM-^HM-^F cells emphasized the importance of nucleosome architecture for proper transcription Examination of nucleosome positions in wild-type and mutants using the MNase-seq method
2012-10-02 | E-GEOD-40451 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the following subset Series: GSE37697: Antisense Transcripts in Mutant Strains GSE40451: Hrp3 controls nucleosome positioning to suppress non-coding transcription in eu- and heterochromatin [MNase-Seq] Refer to individual Series
2012-10-02 | E-GEOD-40453 | biostudies-arrayexpress
Project description:The positioning of the nucleosome by ATP-dependent nucleosome remodelers provides the fundamental chromatin environment for the regulation of diverse cellular processes acting on the underlying DNA. Here, we report that the fission yeast CHD remodeler, Hrp3, is a global regulator that drives higher-order chromatin structure and genomic stability. The loss of Hrp3 resulted in the production of antisense transcripts and perturbation of the nucleosome in an ATPase mutant of Hrp3 was also associated with destabilization of the DNA-histone interaction. Furthermore, the effect of Hrp3 in the pericentric region was found to be accomplished via a physical interaction with Swi6, and appeared to cooperate with other heterochromatin factors for gene silencing. Taken together, our data indicate that a well-positioned nucleosome is important for the spatial-temporal control of transcription-associated processes, and show that this is accomplished by the chromatin remodeler, Hrp3, in fission yeast. Two-condition experiment, Mutant vs Wild-type (control)
2012-05-07 | E-GEOD-37697 | biostudies-arrayexpress
Project description:The positioning of the nucleosome by ATP-dependent nucleosome remodelers provides the fundamental chromatin environment for the regulation of diverse cellular processes acting on the underlying DNA. Here, we report that the fission yeast CHD remodeler, Hrp3, is a global regulator that drives higher-order chromatin structure and genomic stability. The loss of Hrp3 resulted in the production of antisense transcripts and perturbation of the nucleosome in an ATPase mutant of Hrp3 was also associated with destabilization of the DNA-histone interaction. Furthermore, the effect of Hrp3 in the pericentric region was found to be accomplished via a physical interaction with Swi6, and appeared to cooperate with other heterochromatin factors for gene silencing. Taken together, our data indicate that a well-positioned nucleosome is important for the spatial-temporal control of transcription-associated processes, and show that this is accomplished by the chromatin remodeler, Hrp3, in fission yeast.
2012-05-08 | GSE37697 | GEO
Project description:Chromatin remodeling factors and histone chaperones were previously shown to cooperatively affect nucleosome assembly and disassembly processes in vitro. Here we show that S. pombe CHD remodellers, Hrp1 and Hrp3 physically interact with the histone chaperone Nap1. Genome wide analysis of Hrp1, Hrp3 and Nap1 occupancy, combined with nucleosome density measurements in respective mutants revealed that the CHD factors and Nap1 co-localized in particular to promoter regions where they remove nucleosomes near the transcriptional start site. Hrp1 and Hrp3 also regulate nucleosome density in coding regions where they have redundant roles to stimulate transcription. Previously, DNA replication dependent and independent nucleosome disassembly processes have been described. We found that nucleosome density increased in the hrp1 mutant in the absence of DNA replication. Finally, regions where nucleosome density increased in hrp1, hrp3 and nap1 mutants also showed nucleosome density and histone modification changes in HDAC and HAT mutants. Thus, this study revealed an important in vivo role for CHD remodellers and Nap1 in nucleosome disassembly at promoters and coding regions, which are linked to changes in histone acetylation. Keywords: ChIP on CHIP and expression profiling
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Project description:Proper chromatin organization is essential for defining transcription units and maintaining genomic integrity in eukaryotes. Mutations affecting the chromatin structure can lead to increased cryptic transcription and genomic instability. In this study we found that deletion of the Schizosaccharomyces pombe Chd1-type chromatin remodelers, hrp1 and hrp3, causes strong, genome-wide accumulation of antisense transcripts, while the amount of coding mRNA transcripts is mostly unaffected. Nucleosome mapping revealed a specific role for Chd1-remodelers in the positioning of nucleosomes in gene coding regions. While the arrangement of nucleosomes in promoter regions was similar to WT, nucleosome organization within coding regions was remarkably irregular in hrp1∆hrp3∆ strain. We extended our analysis to other mutations associated with enhanced cryptic transcription activity, such as set2∆, alp13∆, and FACT complex subunit pob3∆. While nucleosomes were severely depleted in the pob3∆ strain, nucleosome positioning was less affected. In sharp contrast, nucleosome organization in the alp13∆ and set2∆ strains was indistinguishable from WT. These data indicate multiple mechanisms in the repression of cryptic promoter activity in eukaryotic cells. Genome-wide profiling of H3K9/K14 acetylation Genome-wide expression analysis of either Alp13-, Set2-, Hrp3 or Hrp1 and Hrp3-deficient cells Genome-wide expression analysis of either Hrp1, Hrp3, or Hrp1 and Hrp3-deficient cells Nucleosome mapping experiments
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Project description:Hrp3_Purification from Schizosaccharomyces pombe 972h- Eukaryotic genome is composed of repeating units of nucleosomes to form chromatin arrays. A canonical gene is marked by nucleosome free region (NFR) at its 5’ end followed by uniformly spaced arrays of nucleosomes. In fission yeast we show both biochemically and in vivo that both Hrp1 and Hrp3 are key determinants of uniform spacing of genic arrays.
2014-05-16 | PXD000041 | Pride
Project description:Positioned nucleosomes limit the access of proteins to DNA and implement regulatory features encoded in eukaryotic genomes. Here we generated the first genome-wide nucleosome positioning map for Schizosaccharomyces pombe and annotated transcription start and termination sites genome-wide. Using this resource we found surprising differences compared to the nucleosome organization in the distantly related yeast Saccharomyces cerevisiae [the cerevisiae data has been published by others (PMID: 17873876) and the raw data is deposited at ArrayExpress(E-MEXP-1172)]. DNA sequence guides nucleosome positioning differently, e.g., poly(dA:dT) elements are not enriched in S. pombe nucleosome-depleted regions (NDRs). Regular nucleosomal arrays emanate more asymmetrically, i.e., mainly co-directionally with transcription, from promoter NDRs, but promoters harbouring the histone variant H2A.Z show regular arrays also upstream. Regular nucleosome phasing in S. pombe has a very short repeat length of 154 base pairs, and requires a remodeler, Mit1, conserved in humans but not found in S. cerevisiae. Nucleosome positioning mechanisms are evidently not universal but evolutionarily plastic.
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Project description:Chromatin remodelers influence genetic processes by altering nucleosome occupancy, positioning, and composition. In vitro, yeast ISWI and CHD remodelers require > 20 bp of extranucleosomal DNA for remodeling, but linker DNA in S. cerevisiae averages < 20 bp. To resolve this paradox, we have mapped the genomic distributions of the yeast Isw1, Isw2, and Chd1 remodelers at base-pair resolution. Surprisingly, remodelers are highly enriched at promoter nucleosome depleted regions (5' NDRs), where they bind to regions of extended linker DNA. Remodelers are also enriched in the bodies of genes displaying high nucleosome turnover. We hypothesize that remodelers bind but do not act at 5' NDRs, remaining in physical proximity to gene bodies, where they act on regions of transient nucleosome depletion following transcriptional elongation. We have analyzed the dynamics of yeast ISWI and CHD chromatin remodeler genomic association at base-pair resolution using native chromatin immunoprecipitation followed by sequencing (N-ChIP-seq).
2013-03-01 | E-GEOD-39430 | biostudies-arrayexpress
Project description:Chromatin remodelers influence genetic processes by altering nucleosome occupancy, positioning, and composition. In vitro, yeast ISWI and CHD remodelers require > 20 bp of extranucleosomal DNA for remodeling, but linker DNA in S. cerevisiae averages < 20 bp. To resolve this paradox, we have mapped the genomic distributions of the yeast Isw1, Isw2, and Chd1 remodelers at base-pair resolution. Surprisingly, remodelers are highly enriched at promoter nucleosome depleted regions (5' NDRs), where they bind to regions of extended linker DNA. Remodelers are also enriched in the bodies of genes displaying high nucleosome turnover. We hypothesize that remodelers bind but do not act at 5' NDRs, remaining in physical proximity to gene bodies, where they act on regions of transient nucleosome depletion following transcriptional elongation. We have analyzed the dynamics of yeast ISWI and CHD chromatin remodeler genomic association at base-pair resolution using native chromatin immunoprecipitation followed by sequencing (N-ChIP-seq).
2013-03-01 | E-GEOD-39431 | biostudies-arrayexpress