Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Saccharomyces cerevisiae

ABSTRACT: Sequence-Targeted Nucleosome Sliding in vivo - Transcription Profiling

PROVIDER: PRJNA294375 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR2225070_1.fastq.gz	Fastqsanger.gz
	SRR2225070_2.fastq.gz	Fastqsanger.gz
	SRR2225061_1.fastq.gz	Fastqsanger.gz
	SRR2225061_2.fastq.gz	Fastqsanger.gz
	SRR2225062_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 35

Similar Datasets

Saccharomyces cerevisiae

Project description:Sequence-Targeted Nucleosome Sliding in vivo - Nucleosome Mapping

| PRJNA294376 | ENA

Sequence-Targeted Nucleosome Sliding in vivo

Project description:Sequence-Targeted Nucleosome Sliding in vivo

| PRJNA294374 | ENA

Saccharomyces cerevisiae

Project description:The roles of nucleosome sliding and histone modifications in controlling the fidelity of transcription initiation

| PRJNA658316 | ENA

Nucleosome depletion in Saccharomyces cerevisiae terminator

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

MNase-seq data in 4 modified strains of Saccharomyces cerevisiae, treated or not with 10-Phenanthroline

Project description:We showed that the introduction of a 81bp DNA segment in phase genes leads to the generation of fuzzier nucleosome arrays, but neither to a significant change in the placement of the +1 and –last nucleosomes, nor to a coordinate sliding of nucleosomes. This suggests that irrespectively of other nucleosomes, the +1 and –last nucleosomes are placed in well-defined regions marked by sequence-dependent intrinsic and extrinsic factors, while the rest of the nucleosomes are placed based on periodicity considerations.

2024-10-02 | GSE255857 | GEO

Saccharomyces cerevisiae

Project description:A compendium of nucleosome and transcript profiles reveals determinants of chromatin architecture and transcription [nucleosome profiling]

| PRJNA192581 | ENA

Mechanism of nucleosome positioning, spacing and regularity in Saccharomyces cerevisiae

Project description:Numerous nucleosome remodeling enzymes tightly regulate nucleosome positions in eukaryotic cells. Transcription and statistical positioning of nucleosomes may also contribute to proper nucleosome organization. Individual contributions remain controversial due to strong redundancy of processes acting on the nucleosome landscape. By incisive yeast genome engineering we radically decreased their redundancy. We find the transcriptional machinery to be disruptive of evenly spaced nucleosomes, and proper nucleosome density critical for their biogenesis. INO80 spaces nucleosomes in vivo and positions the first nucleosome covering genes. It requires its Arp8 and Ies2 subunits, but unexpectedly not the Nhp10 module, for spacing. Whereas H2A.Z stimulates INO80 in vitro, its presence is dispensable for INO80 +1 positioning function in vivo. DNA damage, recombination and transposon integration assays suggest that evenly spaced nucleosomes protect cells against genotoxic stress. We derive a unifying model of the biogenesis of the nucleosome landscape and suggest that it evolved not only to regulate but also to protect the genome.

2021-10-20 | GSE141007 | GEO

The telomere-binding protein Tbf1 demarcates snoRNA gene promoters in Saccharomyces cerevisiae

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

Saccharomyces cerevisiae

Project description:In vivo nucleosome occupancy in yeast (MNase-seq)

| PRJNA150155 | ENA

The telomere-binding protein Tbf1 demarcates snoRNA gene promoters in Saccharomyces cerevisiae

2010-05-28 | E-GEOD-20870 | biostudies-arrayexpress