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Chromatin remodelers Isw1 and Chd1 maintain chromatin structure during transcription by preventing histone exchange

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Saccharomyces cerevisiae S288C Saccharomyces cerevisiae

PROVIDER: GSE32071 | GEO | 2012/07/25

SECONDARY ACCESSION(S): PRJNA147595

REPOSITORIES: GEO

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Chromatin remodelers Isw1 and Chd1 maintain chromatin structure during transcription by preventing histone exchange.

Project description:Set2-mediated methylation of histone H3 Lys36 (H3K36) is a mark associated with the coding sequences of actively transcribed genes, but it has a negative role during transcription elongation. It prevents trans-histone exchange over coding regions and signals for histone deacetylation in the wake of RNA polymerase II (RNAPII) passage. We have found that in Saccharomyces cerevisiae the Isw1b chromatin-remodeling complex is specifically recruited to open reading frames (ORFs) by H3K36 methylation through the PWWP domain of its Ioc4 subunit in vivo and in vitro. Isw1b acts in conjunction with Chd1 to regulate chromatin structure by preventing trans-histone exchange from taking place over coding regions. In this way, Isw1b and Chd1 are important in maintaining chromatin integrity during transcription elongation by RNAPII.

| S-EPMC3560298 | biostudies-literature

Chromatin remodelers Isw1 and Chd1 maintain chromatin structure during transcription by preventing histone exchange

Project description:This SuperSeries is composed of the following subset Series: GSE32042: Isw1 and Chd1 maintain chromatin organization during transcription GSE32043: Histone exchange in wildtype, isw1, chd1, isw1 chd1 and ioc4 yeast strains GSE32044: Histone H3 K36me3 in wildtype, isw1 and chd1 yeast strains GSE32045: Isw1 and Chd1 maintain chromatin organization during transcription [AcH4 data] GSE36405: Isw1 and Chd1 maintain chromatin organization during transcription [K56ac data] GSE37158: Isw1 and Chd1 maintain chromatin organization during transcription [isw1 chd1 mutant expression] Refer to individual Series

2012-07-24 | E-GEOD-32071 | biostudies-arrayexpress

Chromatin remodelers Isw1 and Chd1 maintain chromatin structure during transcription by preventing histone exchange

Project description:Chromatin remodelers Isw1 and Chd1 maintain chromatin structure during transcription by preventing histone exchange

| PRJNA147595 | ENA

Chd1 chromatin remodelers maintain nucleosome organization and repress cryptic transcription.

Project description:Chromatin organization is essential for defining transcription units and maintaining genomic integrity in eukaryotes. In this study, we found that deletion of the Schizosaccharomyces pombe Chd1 chromatin remodelers, hrp1 and hrp3, causes strong, genome-wide accumulation of antisense transcripts. Nucleosome mapping revealed a specific role for Chd1 remodelers in the positioning of nucleosomes in gene coding regions. Other mutations associated with enhanced cryptic transcription activity, such as set2Δ, alp13Δ and FACT complex subunit pob3Δ, did not, or only mildly, affect nucleosome positioning. These data indicate several mechanisms in the repression of cryptic promoter activity in eukaryotic cells.

| S-EPMC3492713 | biostudies-literature

The ISW1 and CHD1 ATP-dependent chromatin remodelers compete to set nucleosome spacing in vivo.

Project description:Adenosine triphosphate-dependent chromatin remodeling machines play a central role in gene regulation by manipulating chromatin structure. Most genes have a nucleosome-depleted region at the promoter and an array of regularly spaced nucleosomes phased relative to the transcription start site. In vitro, the three known yeast nucleosome spacing enzymes (CHD1, ISW1 and ISW2) form arrays with different spacing. We used genome-wide nucleosome sequencing to determine whether these enzymes space nucleosomes differently in vivo We find that CHD1 and ISW1 compete to set the spacing on most genes, such that CHD1 dominates genes with shorter spacing and ISW1 dominates genes with longer spacing. In contrast, ISW2 plays a minor role, limited to transcriptionally inactive genes. Heavily transcribed genes show weak phasing and extreme spacing, either very short or very long, and are depleted of linker histone (H1). Genes with longer spacing are enriched in H1, which directs chromatin folding. We propose that CHD1 directs short spacing, resulting in eviction of H1 and chromatin unfolding, whereas ISW1 directs longer spacing, allowing H1 to bind and condense the chromatin. Thus, competition between the two remodelers to set the spacing on each gene may result in a highly dynamic chromatin structure.

| S-EPMC4889916 | biostudies-literature

Isw1 and Chd1 maintain chromatin organization during transcription [isw1 chd1 mutant expression]

Project description:Gene expression microarray experiments to determine the existence of intragenic (cryptic) transcripts in an isw1 chd1 mutant yeast strain.

2012-07-25 | GSE37158 | GEO

Contrasting roles of the RSC and ISW1/CHD1 chromatin remodelers in RNA polymerase II elongation and termination.

Project description:Most yeast genes have a nucleosome-depleted region (NDR) at the promoter and an array of regularly spaced nucleosomes phased relative to the transcription start site. We have examined the interplay between RSC (a conserved essential SWI/SNF-type complex that determines NDR size) and the ISW1, CHD1, and ISW2 nucleosome spacing enzymes in chromatin organization and transcription, using isogenic strains lacking all combinations of these enzymes. The contributions of these remodelers to chromatin organization are largely combinatorial, distinct, and nonredundant, supporting a model in which the +1 nucleosome is positioned by RSC and then used as a reference nucleosome by the spacing enzymes. Defective chromatin organization correlates with altered RNA polymerase II (Pol II) distribution. RSC-depleted cells exhibit low levels of elongating Pol II and high levels of terminating Pol II, consistent with defects in both termination and initiation, suggesting that RSC facilitates both. Cells lacking both ISW1 and CHD1 show the opposite Pol II distribution, suggesting elongation and termination defects. These cells have extremely disrupted chromatin, with high levels of closely packed dinucleosomes involving the second (+2) nucleosome. We propose that ISW1 and CHD1 facilitate Pol II elongation by separating closely packed nucleosomes.

| S-EPMC6396426 | biostudies-literature

Histone exchange in wildtype, isw1, chd1, isw1 chd1 and ioc4 yeast strains

Project description:Histone exchange in wildtype, isw1, chd1, isw1 chd1 and ioc4 yeast strains.

2012-07-25 | GSE32043 | GEO

Isw1 and Chd1 maintain chromatin organization during transcription [isw1 chd1 mutant expression]

Project description:Gene expression microarray experiments to determine the existence of intragenic (cryptic) transcripts in an isw1 chd1 mutant yeast strain. Two color experiment. Mutant/WT. Biological replicates=3. Hybridisation of same samples to strand-specific gene expression arrays.

2012-07-24 | E-GEOD-37158 | biostudies-arrayexpress

Histone exchange in wildtype, isw1, chd1, isw1 chd1 and ioc4 yeast strains

Project description:Histone exchange in wildtype, isw1, chd1, isw1 chd1 and ioc4 yeast strains. Two color experiment. Deletion mutant vs. WT cells. Biological replicates=3 per IP per cell type.

2012-07-24 | E-GEOD-32043 | biostudies-arrayexpress

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