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Clustered regulatory signals at nucleosome-depleted regions punctuate a constant nucleosomal landscape in Schizosaccharomyces pombe [NGS_Illumina]

ABSTRACT: Sequencing of mononucleosomal DNA during asynchronous mitosis and 0, 3 and 5 hours into meiosis in Schizosaccharomyces pombe.

ORGANISM(S): Schizosaccharomyces pombe

PROVIDER: GSE41772 | GEO | 2013/11/25

SECONDARY ACCESSION(S): PRJNA178153

REPOSITORIES: GEO

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Clustered regulatory signals at nucleosome-depleted regions punctuate a constant nucleosomal landscape in Schizosaccharomyces pombe

Project description:Sequencing of mononucleosomal DNA during asynchronous mitosis and 0, 3 and 5 hours into meiosis in Schizosaccharomyces pombe. Two samples from mononucleosomal DNA from asynchronous mitosis (haploid 972 h- and diploid pat1.114) and three samples from 0, 3 and 5 hours into meiosis (from diploid pat1.114) were sequenced (Illumina Genome Analyzer IIx) using the single-end read protocol.

2013-11-25 | E-GEOD-41772 | biostudies-arrayexpress

Clustered regulatory signals at nucleosome-depleted regions punctuate a constant nucleosomal landscape in Schizosaccharomyces pombe [Affymetrix]

2013-11-25 | GSE41770 | GEO

Clustered regulatory signals at nucleosome-depleted regions punctuate a constant nucleosomal landscape in Schizosaccharomyces pombe

Project description:Mononucleosomal DNA analysis of atf1D and pcr1D mutants of Schizosaccharomyces pombe and transcription analysis of exponential wild type 972 h-, atf1D, pcr1D and mitotic diploid pat1.114, and synchronous diploid pat1.114 at 0h, 3h and 5h into meiosis Mononucleosomal DNA vs. genomic input DNA in wildtype 972 h-, atf1D and pcr1D mutants of S. pombe was hybridized to Affymetrix GeneChip 1.0FR tiling microarrays (GPL7715). Total RNA for genome-wide transcription analysis from exponential wild type 972 h-, atf1D, pcr1D and mitotic diploid pat1.114 cells, and from synchronous diploid pat1.114 at 0h, 3h and 5h into meiosis was hybridized to the same microarrays.

2013-11-25 | E-GEOD-41770 | biostudies-arrayexpress

Clustered regulatory elements at nucleosome-depleted regions punctuate a constant nucleosomal landscape in Schizosaccharomyces pombe.

Project description:BACKGROUND: Nucleosomes facilitate the packaging of the eukaryotic genome and modulate the access of regulators to DNA. A detailed description of the nucleosomal organization under different transcriptional programmes is essential to understand their contribution to genomic regulation. RESULTS: To visualize the dynamics of individual nucleosomes under different transcriptional programmes we have generated high-resolution nucleosomal maps in Schizosaccharomyces pombe. We show that 98.5% of the genome remains almost invariable during mitosis and meiosis while remodelling is limited to approximately 1100 nucleosomes in the promoters of a subset of meiotic genes. These inducible nucleosome-depleted regions (NDR) and also those constitutively present in the genome overlap precisely with clusters of binding sites for transcription factors (TF) specific for meiosis and for different functional classes of genes, respectively. Deletion of two TFs affects only a small fraction of all the NDRs to which they bind in vivo, indicating that TFs collectively contribute to NDR maintenance. CONCLUSIONS: Our results show that the nucleosomal profile in S. pombe is largely maintained under different physiological conditions and patterns of gene expression. This relatively constant landscape favours the concentration of regulators in constitutive and inducible NDRs. The combinatorial analysis of binding motifs in this discrete fraction of the genome will facilitate the definition of the transcriptional regulatory networks.

| S-EPMC4046669 | biostudies-literature

Clustered regulatory signals at nucleosome-depleted regions punctuate a constant nucleosomal landscape in Schizosaccharomyces pombe

Project description:This SuperSeries is composed of the SubSeries listed below.

2013-11-25 | GSE41773 | GEO

Clustered regulatory signals at nucleosome-depleted regions punctuate a constant nucleosomal landscape in Schizosaccharomyces pombe

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2013-11-25 | E-GEOD-41773 | biostudies-arrayexpress

A species-specific nucleosomal signature defines a periodic distribution of amino acids in proteins

2015-04-10 | GSE52170 | GEO

A species-specific nucleosomal signature defines a periodic distribution of amino acids in proteins

Project description:Sequencing of mononucleosomal DNA during asynchronous mitosis in Schizosaccharomyces pombe, Schizosaccharomyces octosporus, Schizosaccharomyces japonicus and Saccharomyces cerevisiae Samples from mononucleosomal DNA from asynchronous mitosis of four species of budding (Saccharomyces cerevisiae W303-1a) and fission yeasts (S. pombe wild type 972h-, S. octosporus CBS1804, S. japonicus var. japonicus ade12- FY53) were sequenced (Illumina Genome Analyzer IIx and HiSeq 2500) using the single read and paired end protocol.

2015-04-10 | E-GEOD-52170 | biostudies-arrayexpress

Promoter nucleosome dynamics regulated by signaling through the CTD code

Project description:Sequencing of mononucleosomal DNA from asynchronous cells of Schizosaccharomyces pombe WT and S2A mutant

2015-06-22 | GSE59768 | GEO

Promoter nucleosome dynamics regulated by signaling through the CTD code

Project description:Sequencing of mononucleosomal DNA from asynchronous cells of Schizosaccharomyces pombe WT and S2A mutant Mononucleosomal DNA from asynchronous S. pombe WT (1 sample) and S2A mutant cells (2 samples) were sequenced (Illumina HiSeq 2000) using the single-end read protocol

2015-06-22 | E-GEOD-59768 | biostudies-arrayexpress

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