Nucleosome positioning for 4 yeast species
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ABSTRACT:
PROVIDER: PRJNA130921 | ENA |
REPOSITORIES: ENA
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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 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:To study the evolution of nucleosome positioning we mapped nucleosome positioning in two species of yeasts. Identified differences in nucleosome positioning were classified into cis-based changes or trans-bseed changes based on the pattern of nucleosomes in the hybrid. This analysis was performed for wild-type strains as well as for strains deleted of 5 chromatin regulatoirs allolwing us to examine their roles in determining nucleosome positioning.
2010-03-01 | GSE18939 | GEO
Project description:Nucleosome positioning in H3S57 mutants in yeast
| PRJEB27296 | ENA
Project description:To study the evolution of nucleosome positioning we mapped nucleosome positioning in two species of yeasts. Identified differences in nucleosome positioning were classified into cis-based changes or trans-bseed changes based on the pattern of nucleosomes in the hybrid. This analysis was performed for wild-type strains as well as for strains deleted of 5 chromatin regulatoirs allolwing us to examine their roles in determining nucleosome positioning. Illumina sequencing of mono-nucleosome fragments isolated by MNase digestion. Samples include pooled DNA fragments of S. cerevisiae and S. paradoxus or DNA fragments of the interspecific hybrid. Experiments were performed for WT strains as well as strains deleted of 5 chromatin regulators.
2010-03-01 | E-GEOD-18939 | biostudies-arrayexpress
Project description:In order to test the effect of H3S57 phosphorylation on nucleosome positioning in yeast, nucleosome were mapped in a WT strain, a strain with H3S57A mutation (phospho absent) and a strain H3S57E mutation (phospho mimicking).
2020-12-20 | E-MTAB-6901 | biostudies-arrayexpress
Project description:We report nucleosome poisitioning in Yeast
2014-02-04 | GSE52355 | GEO
Project description:We report nucleosome poisitioning in Yeast Mono-nucleosome DNA was mapped
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Project description:To measure nucleosome positions on a genomic scale, we developed a high-throughput DNA microarray method to identify nucleosomal and linker DNA sequences based on susceptibility of linker DNA to micrococcal nuclease. Nucleosomal DNA was isolated and labeled with Cy3 fluorescent dye (green), and mixed with Cy5-labeled total genomic DNA (red). This mixture was hybridized to microarrays printed with overlapping 50mer oligonucleotide probes tiled across chromosomal regions of interest. Keywords = nucleosome Keywords = yeast Keywords = tiling microrray Keywords: repeat sample
2005-07-14 | GSE2563 | GEO
Project description:Effect of induced Methylation on Nucleosome positioning in yeast. Mnase digested DNA from a control strain and a strain expressing the 4 murine DNMTs were extracted and sequenced on a hiseq 2000
2020-09-30 | E-MTAB-9259 | biostudies-arrayexpress