GEO DataSets

(Submitter supplied) The directionality of gene promoters, the proportion of protein coding over divergent noncoding transcription, is highly variable and regulated. How promoter directionality is controlled remains poorly understood. We show that chromatin remodelling complex RSC, general regulatory factors (GRFs) including transcription factors (TFs) can facilitate promoter directionality by attenuating divergent noncoding transcription. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21656

21 Samples

Download data: TSV

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

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21656

42 Samples

Download data

(Submitter supplied) The directionality of gene promoters, the proportion of protein coding over divergent noncoding transcription, is highly variable and regulated. How promoter directionality is controlled remains poorly understood. We show that chromatin remodelling complex RSC, general regulatory factors (GRFs) including transcription factors (TFs) can facilitate promoter directionality by attenuating divergent noncoding transcription. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21656

21 Samples

Download data: TSV

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

Organism:

Saccharomyces cerevisiae

Type:

Other; Non-coding RNA profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platforms:

GPL17342 GPL21656

49 Samples

Download data: BIGWIG

(Submitter supplied) Eukaryotic cells utilize several mechanisms to ensure that expression of aberrant non-coding RNAs is limited. Gene looping, chromatin modification or remodeling, and RNA surveillance contribute to ensure the fidelity of transcription and limit non-coding transcripts. Here we identify that in Saccharomyces cerevisiae, the transcription factor Rap1 is critical for limiting the expression of aberrant RNAs, particularly near the highly expressed ribosomal protein genes, and characterize them in the context of other non-coding RNAs regulated by chromatin and transcription related factors.

Organism:

Saccharomyces cerevisiae

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL17342

24 Samples

Download data: BIGWIG, TSV

(Submitter supplied) Eukaryotic cells utilize several mechanisms to ensure that expression of aberrant non-coding RNAs is limited. Gene looping, chromatin modification or remodeling, and RNA surveillance contribute to ensure the fidelity of transcription and limit non-coding transcripts. We have identified that the transcription factor Rap1 is critical for limiting the expression of aberrant RNAs, particularly near the highly expressed ribosomal protein genes. more...

Organism:

Saccharomyces cerevisiae

Type:

Other; Expression profiling by high throughput sequencing

Platform:

GPL21656

7 Samples

Download data: BIGWIG

(Submitter supplied) Many active eukaryotic gene promoters exhibit divergent noncoding transcription, but the mechanisms restricting expression of these transcripts are not well understood. Here we demonstrate how a sequence-specific transcription factor represses divergent noncoding transcription at highly expressed genes in yeast. We find that depletion of the transcription factor Rap1 induces noncoding transcription in a large fraction of Rap1 regulated gene promoters. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL17342

18 Samples

Download data: BIGWIG, TSV

(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) Study to detect to genome wide localization of the ATP dependent chromatin remodelling factor Isw2 using ChIP. Keywords: ChIP chip

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL6476

6 Samples

Download data: CEL

(Submitter supplied) To map nucleosome positions in WT and delta isw2 cells Keywords: Nucleosomal DNA hybridization

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL6476

8 Samples

Download data: CEL

(Submitter supplied) To define chromatin structure changes along the yeast genome using microarrays. Nucleosomal DNA from WT and delta isw2 yeast were hybridized and differences in signals were calculated. Keywords: Nucleosomal DNA hybridization

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL6476

4 Samples

Download data: CEL

(Submitter supplied) The classic view of nucleosome organization at active promoters is that two well-positioned nucleosomes flank a nucleosome-depleted region (NDR). However, this view has been recently challenged by contradictory reports as to whether a distinct set of wider (≳150 bp) NDRs instead contain unusually unstable Micrococcal Nuclease-sensitive “fragile” particles, thought to be nucleosomal because of their size. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17342

63 Samples

Download data: BEDGRAPH, PDF

(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) We performed a fluorescent reporter based screen to identify factors determining transcriptional directionality from bidirectional promoters that give rise to a coding and a non-coding transcript. Promoters like these are most frequent in many organisms and non-coding transcription from this origin represents a large fraction of total long non-coding transcripts. We applied NET-seq to compare nascent transcription in yeast wild-type and mutations in the three members of the CAF-I complex. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL13821

8 Samples

Download data: TXT

(Submitter supplied) To assess the organization of regulatory architecture across organisms, we performed ATAC-seq to identify accessible regions of chromatin, H3K4me2 ChIP-seq to measure regulatory status, and PEAT to measure Transcription start sites of stable transcripts in Drosophila S2 cells. For comparison, ATAC-seq for accessible chromatin measurement was performed in whole stage L3 worms.

Organism:

Caenorhabditis elegans; Drosophila melanogaster

Type:

Other; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL19757 GPL19132

8 Samples

Download data: BW

(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:

GPL7550 GPL7542

66 Samples

Download data: GPR

(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