GEO DataSets

(Submitter supplied) Chaperones, nucleosome remodeling complexes and histone acetyltransferases have been implicated in nucleosome disassembly at promoters of particular yeast genes, but whether these co-factors function ubiquitously, and the impact of nucleosome eviction on transcription genome-wide, are poorly understood. We used chromatin immunoprecipitation of histone H3 and RNA polymerase II (Pol II) in mutants lacking single or multiple co-factors to address these issues for ~200 genes belonging to the Gcn4 transcriptome, of which ~70 exhibit marked reductions in H3 promoter occupancy on induction by amino acid starvation. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13821

67 Samples

Download data: BW

(Submitter supplied) The chromatin remodelers (CRs) SWI/SNF and RSC function in evicting promoter nucleosomes at highly expressed yeast genes, particularly those activated by transcription factor Gcn4. Ino80 remodeling complex (Ino80C) can establish nucleosome-depleted regions (NDRs) in reconstituted chromatin, and was implicated in removing histone variant H2A.Z from the -1 and +1 nucleosomes flanking NDRs; however, Ino80C’s function in transcriptional activation in vivo is not well understood. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL23014

101 Samples

Download data: BW

(Submitter supplied) The histone acetyltransferase (HAT) subunit of coactivator complex SAGA, Gcn5, is required for efficient eviction of promoter nucleosomes at certain highly expressed yeast genes, including those activated by transcription factor Gcn4 in amino acid-deprived cells; however, the importance of other HAT complexes in this process was poorly understood. Analyzing mutations that disrupt the integrity or activity of HAT complexes NuA4 or NuA3, or the HAT Rtt109, revealed that only NuA4 acts on par with Gcn5, and functions additively, in evicting and repositioning promoter nucleosomes and stimulating transcription of starvation-induced genes. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL27812 GPL23014

283 Samples

Download data: BIGWIG, BW

(Submitter supplied) ATP-dependent chromatin remodelers (CRs), including SWI/SNF, RSC and Ino80C in budding yeast, are thought to stimulate transcription by repositioning or evicting promoter nucleosomes. The relative importance of these CRs in stimulating activator binding and recruitment of TATA-binding protein (TBP) to promoters is incompletely understood. Examining mutants depleted of the catalytic subunits of these CRs, we determined that RSC and Ino80C stimulate binding of transcription factor Gcn4 to nucleosome-depleted regions, or linkers between genic nucleosomes, at multiple target genes activated by Gcn4 in amino acid-starved cells, frequently by evicting nucleosomes from the Gcn4 binding motifs.  At some genes, SWI/SNF functionally complements RSC, while opposing RSC at others to limit Gcn4 binding. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL23014

71 Samples

Download data: BW

(Submitter supplied) Total H4 and acetyl H4 IP, time course Total H4 and acetyl H4 occupancy, Snf2 occupancy, gene expression analysis Keywords: stress response, time course

Organism:

Saccharomyces cerevisiae

Type:

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

Platform:

GPL5076

167 Samples

Download data: GPR

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

Organism:

Saccharomyces cerevisiae

Type:

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

4 related Platforms

21 Samples

Download data: BW, TXT

(Submitter supplied) ISWI-family chromatin remodelers organize nucleosome arrays, while SWI/SNF-family remodelers (RSC) disorganize and eject nucleosomes, implying an antagonism that is largely unexplored in vivo. Here, we describe two independent genetic screens for rsc suppressors that yielded mutations in the promoter-focused ISW1a complex, or mutations in the ‘basic patch’ of histone H4 (an epitope that regulates ISWI activity), strongly supporting RSC-ISW1a antagonism in vivo. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13821

2 Samples

Download data: BW

(Submitter supplied) ISWI-family chromatin remodelers organize nucleosome arrays, while SWI/SNF-family remodelers (RSC) disorganize and eject nucleosomes, implying an antagonism that is largely unexplored in vivo. Here, we describe two independent genetic screens for rsc suppressors that yielded mutations in the promoter-focused ISW1a complex, or mutations in the ‘basic patch’ of histone H4 (an epitope that regulates ISWI activity), strongly supporting RSC-ISW1a antagonism in vivo. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL13821 GPL13272

7 Samples

Download data: BW

(Submitter supplied) ISWI-family chromatin remodelers organize nucleosome arrays, while SWI/SNF-family remodelers (RSC) disorganize and eject nucleosomes, implying an antagonism that is largely unexplored in vivo. Here, we describe two independent genetic screens for rsc suppressors that yielded mutations in the promoter-focused ISW1a complex, or mutations in the ‘basic patch’ of histone H4 (an epitope that regulates ISWI activity), strongly supporting RSC-ISW1a antagonism in vivo. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by genome tiling array

Platform:

GPL19733

6 Samples

Download data: TXT

(Submitter supplied) ISWI-family chromatin remodelers organize nucleosome arrays, while SWI/SNF-family remodelers (RSC) disorganize and eject nucleosomes, implying an antagonism that is largely unexplored in vivo. Here, we describe two independent genetic screens for rsc suppressors that yielded mutations in the promoter-focused ISW1a complex, or mutations in the ‘basic patch’ of histone H4 (an epitope that regulates ISWI activity), strongly supporting RSC-ISW1a antagonism in vivo. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL4130

2 Samples

Download data: TXT

(Submitter supplied) ISWI-family chromatin remodelers organize nucleosome arrays, while SWI/SNF-family remodelers (RSC) disorganize and eject nucleosomes, implying an antagonism that is largely unexplored in vivo. Here, we describe two independent genetic screens for rsc suppressors that yielded mutations in the promoter-focused ISW1a complex, or mutations in the ‘basic patch’ of histone H4 (an epitope that regulates ISWI activity), strongly supporting RSC-ISW1a antagonism in vivo. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL4130

4 Samples

Download data: TXT

(Submitter supplied) We analyzed the genome-wide expression profile of the wild type strain and the gcn5 mutant (component of the SAGA complex) under basal and cell wall stress (CR during 3 hours) conditions.

Organism:

Schizosaccharomyces pombe; Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL2529

12 Samples

Download data: CEL

(Submitter supplied) The FACT complex and Spt6 are conserved histone chaperones that are recruited to the open reading frames of transcribed genes. In this study, we provide evidence that FACT interaction with acetylated H3 tail is important for its localization to the coding sequences. Pol II CTD kinase Kin28 additionally stimulates FACT recruitment to a subset of genes. Pol II occupancies in the 5’ ends of transcribed genes are greatly reduced on depleting FACT, whereas reduced occupancies at the 3’ ends were observed upon Spt6 depletion indicating that these factors modulate Pol II progression through distinct regions of transcribed coding sequences. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL10930

28 Samples

Download data: TXT

(Submitter supplied) Nucleosomes restrict the access of transcription factors to chromatin. RSC is a SWI/SNF-family chromatin-remodeling complex from yeast that repositions and ejects nucleosomes in vitro. Here, we examined these activities and their importance in vivo. We utilized array-based methods to examine nucleosome occupancy and positioning at more than 200 locations in the genome following the controlled destruction of the catalytic subunit of RSC, Sth1. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL5637

50 Samples

Download data: TXT

(Submitter supplied) Acetylation of Snf2 regulates Swi/Snf recruitment during stress

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL17143 GPL13821

56 Samples

Download data: BW

(Submitter supplied) This is the microarray data accompanying the aforementioned manuscript. Summary: The histone chaperone Vps75 forms a complex with, and stimulates the activity of, the histone acetyltransferase Rtt109. However, Vps75 can also be isolated on its own and might therefore play a role in histone-related cellular processes independently of Rtt109. Using the E-MAP approach, we compared the genetic interaction profiles for VPS75 and RTT109 and found that, whereas deletion of RTT109 behaved like DNA replication/repair mutants, vps75Δ genetically interacted with genes linked to transcriptional regulation. more...

Organism:

Saccharomyces cerevisiae; Saccharomyces cerevisiae W303

Type:

Genome binding/occupancy profiling by genome tiling array

Platforms:

GPL7249 GPL3722

4 Samples

Download data: CEL, TXT