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Schizosaccharomyces pombe

ABSTRACT: Transcription start site positioning is not affected by +1 nucleosome depletion

PROVIDER: PRJNA336018 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR3992210.fastq.gz	Fastqsanger.gz
	SRR3992211.fastq.gz	Fastqsanger.gz
	SRR3992206.fastq.gz	Fastqsanger.gz
	SRR3992207.fastq.gz	Fastqsanger.gz
	SRR3992208.fastq.gz	Fastqsanger.gz

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H2A.Z Mapping During G0/G1 and Mitosis

Project description:We report genome wide mapping of the histone variant H2A.Z during G0/G1 and mitosis in T24 bladder cancer cells. The results show that the broad enrichment pattern of H2A.Z near transcription start sites of active genes is maintained during mitosis. Furthermore, using H2A.Z localization to visualize nucleosome positioning near the start site, we see that the +1 nucleosome of active genes shifts upstream to occupy the transcription start sites during mitosis and the nucleosome depleted region is shortened. H2A.Z is also maintained on the -2 nucleosome which also shifts towrds the transcription start site during mitosis, further contributing to the shorteneing of the nucleosome depleted region. Examination of H2A.Z duing G0/G1 and mitosis in bladder cancer cells

2010-06-24 | E-GEOD-19568 | biostudies-arrayexpress

Schizosaccharomyces pombe

Project description:S. pombe genome-wide nucleosome mapping reveals positioning mechanisms distinct from S. cerevisiae

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H2A.Z Mapping During G0/G1 and Mitosis

2010-06-24 | GSE19568 | GEO

S. pombe genome-wide nucleosome mapping reveals positioning mechanisms distinct from S. cerevisiae

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.

2010-02-01 | GSE16040 | GEO

CHD1 remodelers space nucleosomes in vitro and link regular arrays to 5’ ends of genes in S. Pombe

Project description:Nucleosome positioning governs access to eukaryotic genomes. Many genes show a stereotypic organisation at their 5’ end: a nucleosome free region just upstream of the transcription start site (TSS) followed by a regular nucleosomal array over the coding region. The determinants for this pervasive pattern are unclear, but nucleosome remodeling ATPases likely are critical. Now we employ deletion mutants to study the role of nucleosome remodeling ATPases in global nucleosome positioning in S. pombe and the corresponding changes in expression patterns. We find a striking evolutionary shift in remodeling enzyme usage between budding and fission yeast. The S. pombe RSC remodeling complex seems not involved in nucleosome positioning, despite its prominent role in S. cerevisiae. While lacking ISWI-type remodelers, S. pombe has two CHD1-type ATPases, Hrp1 and Hrp3. We demonstrate nucleosome spacing activity for both in vitro, and together they are essential for linking regular genic arrays to most TSSs in vivo. Impaired chromatin may but need not lead to changes in transcription. The absence of both causes changed expression for about 20% and increased antisense transcription for 15% of all annotated elements.

2012-10-11 | GSE41024 | GEO

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