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Saccharomyces cerevisiae

ABSTRACT: Effects of Histone H3 depletion on nucleosome occupancy and positioning through the S. cerevisiae genome [RNA_seq]

OTHER RELATED OMICS DATASETS IN: GSE29294

PROVIDER: PRJNA142815 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR223526.fastq.gz	Fastqsanger.gz
	SRR223527.fastq.gz	Fastqsanger.gz
	SRR223528.fastq.gz	Fastqsanger.gz
	SRR223529.fastq.gz	Fastqsanger.gz
	SRR223530.fastq.gz	Fastqsanger.gz

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Project description:H3 ChIP and input DNA were hybridized to Affymetrix GeneChip S. cerevisiae Tiling 1.0R Array Genome-wide mapping of nucleosomes generated by micrococcal nuclease (MNase) suggests that yeast promoter and terminator regions are very depleted of nucleosomes, predominantly because their DNA sequences intrinsically disfavor nucleosome formation. However, MNase has strong DNA sequence specificity that favors cleavage at promoters and terminators and accounts for some of the correlation between occupancy patterns of nucleosomes assembled in vivo and in vitro. Using an improved method for measuring nucleosome occupancy in vivo that does not involve MNase, we confirm that promoter regions are strongly depleted of nucleosomes, but find that terminator regions are much less depleted than expected. Unlike at promoter regions, nucleosome occupancy at terminators is strongly correlated with the orientation of and distance to adjacent genes. In addition, nucleosome occupancy at terminators is strongly affected by growth conditions, indicating that it is not primarily determined by intrinsic histone-DNA interactions. Rapid removal of RNA polymerase II (Pol II) causes increased nucleosome occupancy at terminators, strongly suggesting a transcription-based mechanism of nucleosome depletion. However, the distinct behavior of terminator regions and their corresponding coding regions suggests that nucleosome depletion at terminators is not simply associated with passage of Pol II, but rather involves a distinct mechanism linked to 3’ end formation.

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Effects of Histone H3 depletion on nucleosome occupancy and positioning through the S. cerevisiae genome

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Project description:We report change in the nucleosome occupancy and accessibility upon deletion of ATP-dependent chromatin remodellers (ISW1, ISW2 & CHD1) in Saccharomyces cerevisiae.

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Divergent residues within histone H3 define a unique chromatin structure in S. cerevisiae

Project description:Histones are among the most conserved proteins known, but organismal differences do exist. In this study we examined the contribution that divergent amino acids within histone H3 make to cell growth and chromatin structure in S. cerevisiae. We show that, while amino acids that define histone H3.3 are dispensable for yeast growth, substitution of residues within the histone H3 alpha 3 helix with the human counterparts results in a severe growth defect. Mutations within this domain also result in altered nucleosome positioning, both in vivo and in vitro, which is accompanied by increased preference for nucleosome favoring sequences. These results suggest that divergent amino acids within the histone H3 alpha 3 helix play organismal roles in defining chromatin structure.

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MEDIATOR subunit med8 binding in Saccharomyces cerevisiae

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