GEO DataSets

(Submitter supplied) We identify the cis and trans determinants of nucleosome positioning using a functional evolutionary approach involving S. cerevisiae strains containing large genomic regions from other yeast species. In a foreign species, nucleosome depletion at promoters is maintained over poly(dA:dT) tracts, whereas internucleosome spacing and all other aspects of nucleosome positioning tested are not. Interestingly, the locations of the +1 nucleosome and RNA start sites shift in concert. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9134

5 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platform:

GPL13272

20 Samples

Download data: BED, TXT, WIG

(Submitter supplied) Experiments performed over the past three decades have shown that nucleosomes are transcriptional repressors. In Saccharomyces cerevisiae, depletion of histone H4 results in the genome-wide transcriptional de-repression of hundreds genes. The mechanism of de-repression is hypothesized to be rooted directly in chromatin changes. To test this, we reproduced classical H4 depletion experiments by conditional repression of all histone H3 transcription, which depletes the supply of nucleosomes in vivo. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13272

6 Samples

Download data: WIG

(Submitter supplied) Experiments performed over the past three decades have shown that nucleosomes are transcriptional repressors. In Saccharomyces cerevisiae, depletion of histone H4 results in the genome-wide transcriptional de-repression of hundreds genes. The mechanism of de-repression is hypothesized to be rooted directly in chromatin changes. To test this, we reproduced classical H4 depletion experiments by conditional repression of all histone H3 transcription, which depletes the supply of nucleosomes in vivo. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13272

8 Samples

Download data: BED, TXT

(Submitter supplied) Experiments performed over the past three decades have shown that nucleosomes are transcriptional repressors. In Saccharomyces cerevisiae, depletion of histone H4 results in the genome-wide transcriptional de-repression of hundreds genes. The mechanism of de-repression is hypothesized to be rooted directly in chromatin changes. To test this, we reproduced classical H4 depletion experiments by conditional repression of all histone H3 transcription, which depletes the supply of nucleosomes in vivo. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13272

6 Samples

Download data: BED, TXT

(Submitter supplied) The positioning of nucleosomes within the coding regions of eukaryotic genes is aligned with respect to transcriptional start sites. This organization is likely to influence many genetic processes, requiring access to the underlying DNA. Here we show that the combined action of Isw1 and Chd1 nucleosome spacing enzymes is required to maintain this organization. In the absence of these enzymes regular positioning of the majority of nucleosomes is lost. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL14009

3 Samples

Download data: TXT

(Submitter supplied) ChIP-chip assays to determine the localisation of 3xFLAG tagged Isw1 in wild-type yeast.

Organism:

Saccharomyces cerevisiae S288C; Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL13972

3 Samples

Download data: TXT

(Submitter supplied) The positioning of nucleosomes within the coding regions of eukaryotic genes is aligned with respect to transcriptional start sites. This organization is likely to influence many genetic processes, requiring access to the underlying DNA. Here we show that the combined action of Isw1 and Chd1 nucleosome spacing enzymes is required to maintain this organization. In the absence of these enzymes regular positioning of the majority of nucleosomes is lost. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9134

5 Samples

Download data: BW

(Submitter supplied) Chromatin remodelers regulate genes by organizing nucleosomes around promoters, but their individual contributions are obfuscated by the complex in vivo milieu of factor redundancy and indirect effects. Genome-wide reconstitution of promoter nucleosome organization with purified proteins resolves this problem and is therefore a critical goal. Here we reconstitute four stages of nucleosome architecture using purified components: Yeast genomic DNA, histones, sequence-specific Abf1/Reb1, and remodelers RSC, ISW2, INO80, and ISW1a. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL19756 GPL18085 GPL13821

92 Samples

Download data: BEDGRAPH, TXT

(Submitter supplied) 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)]. more...

Organism:

Saccharomyces cerevisiae; Schizosaccharomyces pombe

Type:

Genome binding/occupancy profiling by genome tiling array; Expression profiling by array

Platforms:

GPL7715 GPL2529

16 Samples

Download data: BAR, CEL

(Submitter supplied) Using an integrated analysis of chromatin remodeler binding in unperturbed cells and nucleosome displacement activity upon rapid remodeler depletion or degradation, we investigate the interplay between these enzymes and their functional consequences. We show that many promoters are acted upon by multiple remodelers that operate either cooperatively or in opposition to determine the precise location of the key transcription start site-associated +1 nucleosome. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other; Methylation profiling by high throughput sequencing

Platforms:

GPL21656 GPL17342

82 Samples

Download data: BIGWIG, BW

(Submitter supplied) 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.

Organism:

Saccharomyces cerevisiae x Saccharomyces paradoxus; Saccharomyces cerevisiae; Saccharomyces paradoxus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL9613 GPL9611

12 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Saccharomyces cerevisiae S288C; Saccharomyces cerevisiae W303; Saccharomyces cerevisiae

Type:

Expression profiling by array; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL17342 GPL11232

64 Samples

Download data: BW, TXT

(Submitter supplied) Here we present evidence that precise positioning of the +1 promoter nucleosome in yeast is critical for efficient TBP binding and pre-initiation complex assembly, and is determined, at least in part, by the action of two key factors, the essential chromatin remodeler RSC and one (or more) of a small set of ubiquitous pioneer transcription factors (PTFs). Despite their widespread co-localization, we show that RSC and PTFs often act independently to generate accessible chromatin. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17342

52 Samples

Download data: BW

(Submitter supplied) Here we present evidence that precise positioning of the +1 promoter nucleosome in yeast is critical for efficient TBP binding and pre-initiation complex assembly, and is determined, at least in part, by the action of two key factors, the essential chromatin remodeler RSC and one (or more) of a small set of ubiquitous pioneer transcription factors (PTFs). Despite their widespread co-localization, we show that RSC and PTFs often act independently to generate accessible chromatin. more...

Organism:

Saccharomyces cerevisiae W303; Saccharomyces cerevisiae; Saccharomyces cerevisiae S288C

Type:

Expression profiling by array

Platform:

GPL11232

12 Samples

Download data: TXT

(Submitter supplied) Arrays of regularly spaced nucleosomes dominate chromatin and are often phased, i.e., aligned at reference sites like active promoters. How distances between nucleosomes and distances between phasing sites and nucleosomes are determined remained unclear, specifically, the role of ATP dependent chromatin remodelers in it. Here, we used a genome-wide reconstitution system to probe how yeast remodelers generate phased nucleosome arrays. more...

Organism:

Escherichia coli; Schizosaccharomyces pombe; Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL20045 GPL18085 GPL22681

450 Samples

Download data: BED, BW, CSV, RDS, TAB, TXT

(Submitter supplied) The mechanistics by which ATP-dependent chromatin remodelers process (epi)genetic information to generate hallmark features of chromatin are fundamental for genome regulation. Here, we advance whole-genome reconstitutions into a fully definable, recombinant approach for probing how remodelers determine nucleosome positioning. Using wild type and structure-guided mutant versions of the Saccharomyces cerevisiae 15-subunit INO80 remodeler, we show that INO80-intrinsic nucleosome positioning relies on direct DNA shape read-out. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18085

91 Samples

Download data: BW, RDA, TAB, TXT

(Submitter supplied) We assess the role of intrinsic histone-DNA interactions by mapping nucleosomes assembled in vitro on genomic DNA. Nucleosomes strongly prefer yeast DNA over E. coli DNA, indicating that the yeast genome evolved to favor nucleosome formation. Many yeast promoter and terminator regions intrinsically disfavor nucleosome formation, and nucleosomes assembled in vitro display strong rotational positioning. more...

Organism:

Saccharomyces cerevisiae; Escherichia coli

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL10839

3 Samples

Download data: TXT, WIG

(Submitter supplied) Nucleosome positioning governs access to eukaryotic genomes. Many genes show a stereotypic organisation at their 5’ end: a nucleosome free region just upstream of the transcription start site (TSS) followed by a regular nucleosomal array over the coding region. The determinants for this pervasive pattern are unclear, but nucleosome remodeling ATPases likely are critical. Now we employ deletion mutants to study the role of nucleosome remodeling ATPases in global nucleosome positioning in S. more...

Organism:

Schizosaccharomyces pombe

Type:

Expression profiling by genome tiling array; Genome binding/occupancy profiling by genome tiling array

Platform:

GPL7715

40 Samples

Download data: CEL, TXT

(Submitter supplied) The chromatin architecture of eukaryotic gene promoters is generally characterized by a nucleosome-free region (NFR) flanked by at least one H2A.Z variant nucleosome. Computational predictions of nucleosome positions based on thermodynamic properties of DNA-histone interactions have met with limited success. Here we show that the action of the essential RSC remodeling complex in S. cerevisiae helps explain the discrepancy between theory and experiment. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by genome tiling array; Expression profiling by array

Platforms:

GPL7542 GPL7550

66 Samples

Download data: GPR