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Saccharomyces cerevisiae

ABSTRACT: Sequence-Targeted Nucleosome Sliding in vivo - Nucleosome Mapping

PROVIDER: PRJNA294376 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR2225050_1.fastq.gz	Fastqsanger.gz
	SRR2225050_2.fastq.gz	Fastqsanger.gz
	SRR2225051_1.fastq.gz	Fastqsanger.gz
	SRR2225051_2.fastq.gz	Fastqsanger.gz
	SRR2225052_1.fastq.gz	Fastqsanger.gz

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Saccharomyces cerevisiae

Project description:Sequence-Targeted Nucleosome Sliding in vivo - Transcription Profiling

| PRJNA294375 | ENA

Sequence-Targeted Nucleosome Sliding in vivo

Project description:Sequence-Targeted Nucleosome Sliding in vivo

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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 W303

Project description:S. cerevisiae Nucleosome mapping

| PRJNA205194 | ENA

Saccharomyces cerevisiae

Project description:DMS-seq for in vivo genome-wide mapping of protein–DNA interactions and nucleosome centers

| PRJNA359195 | ENA

Saccharomyces cerevisiae

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

| PRJNA658316 | ENA

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)

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Absolute nucleosome occupancy map for the Saccharomyces cerevisiae genome [ORE-seq]

Project description:Mapping of nucleosomes, the basic DNA packaging unit in eukaryotes, is fundamental for understanding genome regulation as nucleosomes modulate DNA access by their positioning along the genome. A cell population nucleosome map requires two observables: nucleosome positions along the DNA (“Where?”) and nucleosome occupancies across the population (“In how many cells?”). All available genome-wide nucleosome mapping techniques are yield methods as they score either nucleosomal (e.g., MNase-seq, chemical cleavage-seq) or non-nucleosomal (e.g., ATAC-seq) DNA but lose track of the total DNA population for each genomic region. Therefore, they only provide nucleosome positions and maybe compare relative occupancies between positions but cannot measure absolute nucleosome occupancy, which is the fraction of all DNA molecules occupied at a given position and time by a nucleosome. Here, we established two orthogonal and thereby crossvalidating approaches to measure absolute nucleosome occupancy across the Saccharomyces cerevisiae genome via restriction enzymes and DNA methyltransferases. The resulting high-resolution (9 bp) map shows uniform absolute occupancies. Most nucleosome positions are occupied in most cells: 97% of all nucleosomes called by chemical cleavage-seq have a mean absolute occupancy of 90 ± 6% (± SD). Depending on nucleosome position calling procedures, there are 57-60,000 nucleosomes per yeast cell. The few low absolute occupancy nucleosomes do not correlate with highly transcribed gene bodies, but with increased presence of the nucleosome-evicting RSC chromatin remodeling complex there and are enriched upstream of highly transcribed or regulated genes. Our work provides a quantitative method and reference frame in absolute terms for future chromatin studies.

2019-11-27 | GSE141056 | GEO

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