Saccharomyces cerevisiae
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA133373 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:We report change in the nucleosome occupancy and accessibility upon deletion of ATP-dependent chromatin remodellers (ISW1, ISW2 & CHD1) in Saccharomyces cerevisiae.
2024-02-08 | GSE220880 | GEO
Project description:S. cerevisiae Nucleosome mapping
| PRJNA205194 | ENA
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.
2010-09-21 | GSE23778 | GEO
Project description:Cell cycle dependent nucleosome occupancy at cohesin binding sites in yeast chromosomes
| PRJNA101013 | ENA
Project description:Nucleosome depletion in Saccharomyces cerevisiae terminator
| PRJNA130623 | ENA
Project description:The relationship between chromatin structure and transposable element (TE) integration is a fundamental question as nucleosomes can either mediate or inhibit TE insertion. The Ty1 element in Saccharomyces cerevisiae preferentially inserts upstream of RNA Polymerase III-transcribed genes, in a manner coincident with nucleosome positioning. Ty1 insertion positions have largely been inferred from nucleosome occupancy maps, but this approach is imperfect. Nucleosome occupancy maps are typically generated from wild-type Saccharomyces cerevisiae cells grown in standard conditions. Many Ty1 studies rely on a galactose-inducible expression system and it is not yet known if Ty1 overexpression from the GAL1 promoter itself alters nucleosome organization under inducing conditions. Here, we used a galactose-inducible Ty1 expression system and genome-wide MNase-seq to determine whether Ty1 donor plasmid transformation and overexpression alter nucleosome occupancy. We find that changes in carbon source do not substantially alter genome-wide nucleosome organization. In contrast, galactose induction of Ty1 expression revealed time-dependent changes in nucleosome occupancy. Nucleosome organization is unchanged across pre-induction, 6-hour galactose exposure, and post-induction repressing conditions, but nucleosome occupancy shifted at 12 and 24 hours, with changes evident at both Pol II and tRNA genes. We also found that Ty1 integration events are rare at early time points, emerge by 12 hours, and accumulate substantially by 24 hours. Ty1 preferentially targets nucleosomal DNA, but prolonged induction shifts insertion positions relative to nucleosomes. We also find that Ty1 preferentially targets nucleosomal DNA that lies in close proximity to histones, with this preference showing time-dependent shifts during induction.
2026-07-29 | GSE337686 | GEO
Project description:Genome-wide nucleosome position maps in Saccharomyces cerevisiae
| PRJNA136495 | ENA
Project description:Nucleosome mapping in Saccharomyces cerevisiae in different conditions
| PRJNA171742 | ENA
Project description:The majority of Saccharomyces cerevisiae snoRNA promoters contain an aRCCCTaa sequence motif located at the upstream border of a TATA-containing nucleosome-free region. Genome-wide ChIP-seq analysis showed that these motifs are bound in vivo by Tbf1, a telomere-binding protein known to recognize mammalian-like T2AG3 repeats at sub-telomeric regions. Tbf1 has over 100 additional promoter targets, including the TBF1 gene itself. Tbf1 is required for full snoRNA expression, yet it does not influence nucleosome positioning at snoRNA promoters.
2010-05-28 | GSE20870 | GEO