Genome-wide nucleosome position data for 3 yeast species
Ontology highlight
ABSTRACT:
ORGANISM(S): Saccharomyces cerevisiae Schizosaccharomyces pombe Candida albicans
PROVIDER: GSE28839 | GEO | 2011/08/01
SECONDARY ACCESSION(S): PRJNA140615
REPOSITORIES: GEO
Similar Datasets
Project description:Genome-wide nucleosome position data for wildtype and mutant strains in S. cerevisiae, C. albicans, and S. pombe Illumina sequencing of mononucleosomal DNA isolated from mid-log cultures grown in rich medium (abbreviated CM, in house recipe). S. pombe samples were grown in YES medium at permissive temperature (30C) and restrictive temperature (35C)
2011-08-01 | E-GEOD-28839 | biostudies-arrayexpress
Project description:Genome-wide nucleosome position data for 12 yeast species
| PRJNA128881 | ENA
Project description:Genome-wide nucleosome position data for 3 yeast species
| PRJNA140615 | ENA
Project description:We describe the genome-wide nucleosome profiles of four related yeast species. All species display the same global organization features first described in S. cerevisiae: a stereotypical nucleosome organization along genes, and the classification of promoters into these which contain or lack a pronounced Nucleosome Depleted region (NDR), with the latter displaying a more dynamic pattern of gene expression. This global similarity, however, does not reflect a static evolutionary pattern, as nucleosome positioning at specific genes diverged rapidly leaving practically no similarity between S. cerevisiae and C. glabrata orthologs (~50 Myr). We show that this rapid divergence in nucleosome positioning contrasts a conserved pattern of gene expression, consistent with the idea that divergence of nucleosome patterns has a limited effect on gene expression as many different configurations can support the same regulatory outcome.
2011-12-09 | GSE23577 | GEO
Project description:We mapped nucleosome positions genome-wide in 12 Ascomycetes
2010-07-06 | GSE22211 | GEO
Project description:We describe the genome-wide nucleosome profiles of four related yeast species. All species display the same global organization features first described in S. cerevisiae: a stereotypical nucleosome organization along genes, and the classification of promoters into these which contain or lack a pronounced Nucleosome Depleted region (NDR), with the latter displaying a more dynamic pattern of gene expression. This global similarity, however, does not reflect a static evolutionary pattern, as nucleosome positioning at specific genes diverged rapidly leaving practically no similarity between S. cerevisiae and C. glabrata orthologs (~50 Myr). We show that this rapid divergence in nucleosome positioning contrasts a conserved pattern of gene expression, consistent with the idea that divergence of nucleosome patterns has a limited effect on gene expression as many different configurations can support the same regulatory outcome. Nucleosomes from 4 different yeast species were isolated and sequenced using the Illumina GAII platform. Replicates were performed for 3 of the species
2011-12-09 | E-GEOD-23577 | biostudies-arrayexpress
Project description:We mapped nucleosome positions genome-wide in 12 Ascomycetes Illumina sequencing of mononucleosomal DNA isolated from mid-log cultures grown in rich medium (abbreviated CM, in house recipe)
2010-07-06 | E-GEOD-22211 | biostudies-arrayexpress
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
Project description:We tracked the fate of labelled nucleosomes through DNA replication, and established that nucleosomes present at a locus remembered their position during DNA replication. The replication-associated histone chaperones DPB3 and MCM2 were essential for nucleosome position memory, and in the absence of both DPB3 and MCM2 histone chaperone activity nucleosomes did not remember their position. Using the same approach, we tested the model that transcription results in retrograde transposition of nucleosomes along a transcription unit. We found no evidence of retrograde transposition. Our results suggest that nucleosomes have the capacity to transmit epigenetic memory across mitotic generations with exquisite spatial fidelity.
2019-12-01 | GSE135102 | GEO
Project description:This SuperSeries is composed of the following subset Series: GSE22191: Absolute expression level of Debaryomyces hansenii genes GSE22192: Absolute expression level of Yarrowia lipolytica genes GSE22193: Absolute expression level of Saccharomyces paradoxus genes GSE22194: Absolute expression level of Candida glabrata genes GSE22197: Absolute expression level of Candida albicans genes GSE22198: Absolute expression level of Kluyveromyces lactis genes GSE22199: Absolute expression level of Kluyveromyces waltii genes GSE22200: Absolute expression level of Saccharomyces castellii genes GSE22201: Absolute expression level of Saccharomyces mikatae genes GSE22202: Absolute expression level of Saccharomyces kluyveryii genes GSE22204: Absolute expression level of Saccharomyces cerevisiae genes GSE22205: Absolute expression level of Saccharomyces bayanus genes GSE22211: Genome-wide nucleosome position data for 12 yeast species Refer to individual Series
2010-07-05 | E-GEOD-21960 | biostudies-arrayexpress