Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Dynamics of yeast ISWI and CHD chromatin remodeler genomic association (part 2)

ABSTRACT: 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).

ORGANISM(S): Saccharomyces cerevisiae

SUBMITTER: Jorja Henikoff

PROVIDER: E-GEOD-39431 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

ISWI and CHD chromatin remodelers bind promoters but act in gene bodies.

Zentner Gabriel E GE Tsukiyama Toshio T Henikoff Steven S

PLoS genetics 20130228 2

ATP-dependent nucleosome remodelers influence genetic processes by altering nucleosome occupancy, positioning, and composition. In vitro, Saccharomyces cerevisiae ISWI and CHD remodelers require ∼30-85 bp of extranucleosomal DNA to reposition nucleosomes, but linker DNA in S. cerevisiae averages <20 bp. To address this discrepancy between in vitro and in vivo observations, we have mapped the genomic distributions of the yeast Isw1, Isw2, and Chd1 remodelers at base-pair resolution on native chro ...[more]

PMID: 23468649

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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 hrp1M-bM-^HM-^Fhrp3M-bM-^HM-^F strain. We extended our analysis to other mutations associated with enhanced cryptic transcription activity, such as set2M-bM-^HM-^F, alp13M-bM-^HM-^F, and FACT complex subunit pob3M-bM-^HM-^F. While nucleosomes were severely depleted in the pob3M-bM-^HM-^F strain, nucleosome positioning was less affected. In sharp contrast, nucleosome organization in the alp13M-bM-^HM-^F and set2M-bM-^HM-^F 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 ChIP for the detection of the genome-wide acetylation profile of H3K9/K14 was performed for a wildtype strain and the deletion strains of Set2, Alp13 and the double knock-out of Hrp1 and Hrp3. Each experiment was performed twice in biological replicates All experiments were performed twice in biological replicates, except for the expression array of set2M-NM-^T. The replicates of hrp3M-NM-^T and hrp1M-NM-^Thrp3M-NM-^T were performed with a slightly different array design All experiments were performed twice in biological replicates. The replicates of hrp3M-NM-^T and hrp1M-NM-^Thrp3M-NM-^T were performed with a slightly different array design MNase treated sample were comparatively hybridized with genomic DNA of corresponding strain, WT, hrp1d hrp3d, pob3d in biological duplicates, set2d, alp13d, mit1d, hrp1d, hrp3d analysis was performed once

Dataset Information

Dynamics of yeast ISWI and CHD chromatin remodeler genomic association (part 2)

Publications

ISWI and CHD chromatin remodelers bind promoters but act in gene bodies.

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