GEO DataSets

(Submitter supplied) R-loops are transcription by-products that may constitute a threat to genome integrity. In addition to specific enzymes to remove them, eukaryotes rely on a number of mRNP biogenesis factors such as the THO complex, to prevent co-transcriptional R-loop formation. We show in Saccharomyces cerevisiae that R-loops are tightly and specifically linked with histone H3-Ser10 phosphorylation (H3S10P), a mark of chromatin condensation. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL7250

6 Samples

Download data: BAR, BED, CEL

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

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by genome tiling array

Platforms:

GPL4131 GPL2625 GPL3737

33 Samples

Download data: TXT

(Submitter supplied) Chromatin plays roles in processes governed by different time scales. To assay the dynamic behaviour of chromatin in living cells, we used genomic tiling arrays to measure histone H3 turnover in G1-arrested S. cerevisiae at single-nucleosome resolution over 4% of the genome, and over the entire genome at lower (~265 bp) resolution. We find that nucleosomes at promoters are replaced more rapidly than at coding regions, and that replacement rates over coding regions correlate with polymerase density. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL3737

2 Samples

Download data: TXT

(Submitter supplied) Chromatin plays roles in processes governed by different time scales. To assay the dynamic behaviour of chromatin in living cells, we used genomic tiling arrays to measure histone H3 turnover in G1-arrested S. cerevisiae at single-nucleosome resolution over 4% of the genome, and over the entire genome at lower (~265 bp) resolution. We find that nucleosomes at promoters are replaced more rapidly than at coding regions, and that replacement rates over coding regions correlate with polymerase density. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL4131

2 Samples

Download data: TXT

(Submitter supplied) Chromatin plays roles in processes governed by different time scales. To assay the dynamic behaviour of chromatin in living cells, we used genomic tiling arrays to measure histone H3 turnover in G1-arrested S. cerevisiae at single-nucleosome resolution over 4% of the genome, and over the entire genome at lower (~265 bp) resolution. We find that nucleosomes at promoters are replaced more rapidly than at coding regions, and that replacement rates over coding regions correlate with polymerase density. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL4131

2 Samples

Download data: TXT

(Submitter supplied) Chromatin plays roles in processes governed by different time scales. To assay the dynamic behaviour of chromatin in living cells, we used genomic tiling arrays to measure histone H3 turnover in G1-arrested S. cerevisiae at single-nucleosome resolution over 4% of the genome, and over the entire genome at lower (~265 bp) resolution. We find that nucleosomes at promoters are replaced more rapidly than at coding regions, and that replacement rates over coding regions correlate with polymerase density. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL4131

4 Samples

Download data: TXT

(Submitter supplied) Chromatin plays roles in processes governed by different time scales. To assay the dynamic behaviour of chromatin in living cells, we used genomic tiling arrays to measure histone H3 turnover in G1-arrested S. cerevisiae at single-nucleosome resolution over 4% of the genome, and over the entire genome at lower (~265 bp) resolution. We find that nucleosomes at promoters are replaced more rapidly than at coding regions, and that replacement rates over coding regions correlate with polymerase density. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL3737

7 Samples

Download data: TXT

(Submitter supplied) Chromatin plays roles in processes governed by different time scales. To assay the dynamic behaviour of chromatin in living cells, we used genomic tiling arrays to measure histone H3 turnover in G1-arrested S. cerevisiae at single-nucleosome resolution over 4% of the genome, and over the entire genome at lower (~265 bp) resolution. We find that nucleosomes at promoters are replaced more rapidly than at coding regions, and that replacement rates over coding regions correlate with polymerase density. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL2625

8 Samples

Download data: TXT

(Submitter supplied) Chromatin plays roles in processes governed by different time scales. To assay the dynamic behaviour of chromatin in living cells, we used genomic tiling arrays to measure histone H3 turnover in G1-arrested S. cerevisiae at single-nucleosome resolution over 4% of the genome, and over the entire genome at lower (~265 bp) resolution. We find that nucleosomes at promoters are replaced more rapidly than at coding regions, and that replacement rates over coding regions correlate with polymerase density. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL2625

8 Samples

Download data: TXT

(Submitter supplied) We mapped ssDNA formation in WT and hpr1delta cells at permissive (30C) and non-permissive (37C) temperature. We showed that hpr1 cells accumulate ssDNA show elevated levels of ssDNA at centromeric regions. Additionally, we show replication fork-associated ssDNA at origins of replication is more confined to the origins in hpr1 cells than WT cells, suggesting a defect in replication fork progression.

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL10930

8 Samples

Download data: TXT, XLSX

(Submitter supplied) The conserved FACT (FAcilitates Chromatin Transcription) complex is a chromatin-reorganizing complex that promotes RNAPII transcription through chromatin templates by interacting with histones. It facilitates promoter activation by nucleosome eviction, and transcription elongation by nucleosome disruption and reassembly ahead and behind the RNAP. It also has a role in replication not fully understood yet. more...

Organism:

Saccharomyces cerevisiae; Schizosaccharomyces pombe

Type:

Expression profiling by array

Platform:

GPL2529

9 Samples

Download data: CEL

(Submitter supplied) Transcription is a major obstacle for replication fork progression and transcription-replication collisions constitute a main cause of genome instability. At a genome-wide scale these obstacles can be detected by the accumulation of the replicative Rrm3 helicase required for RF progression through protein obstacles. Here we show that FACT, a chromatin-reorganizing complex that swaps nucleosomes around the RNA polymerase during transcription elongation and that also has a role in replication, is needed to resolve transcription-replication conflicts in Saccharomyces cerevisiae. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL7250

5 Samples

Download data: BAR, BED, CEL

(Submitter supplied) The stability of the genome is occasionally challenged by the formation of DNA-RNA hybrids and R-loops, which can be influenced by the chromatin context. This is mainly due to the fact that DNA-RNA hybrids hamper the progression of replication forks, leading to fork stalling and, ultimately, DNA breaks. Through a specific screening of chromatin modifiers performed in the yeast Saccharomyces cerevisiae, we have found that the Rtt109 histone acetyltransferase is involved in several steps of R-loop-metabolism and their associated genetic instability. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19756

14 Samples

Download data: WIG

(Submitter supplied) Argonaute proteins and their small RNA co-factors short interfering RNAs (siRNAs) are known to inhibit gene expression at the transcriptional and post-transcriptional levels. In Caenorhabditis elegans, the Argonaute CSR-1 binds thousands of endogenous siRNAs (endo-siRNAs) antisense to germline transcripts and associates with chromatin in a siRNA-dependent manner. However, its role in gene expression regulation remains controversial. more...

Organism:

Caenorhabditis elegans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13657

8 Samples

Download data: BW

(Submitter supplied) The formation of R-loops is a natural consequence of the transcription process, caused by invasion of the DNA duplex by nascent transcripts. These structures have been considered rare transcriptional by-products with potential harmful effects on genome integrity, due to the fragility of the displaced DNA coding strand. However R-loops may also possess beneficial effects as their widespread formation has been detected over CpG island promoters in human genes. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11154

4 Samples

Download data: NARROWPEAK

(Submitter supplied) Chromatin accessibility, a crucial component of genome regulation, has mostly been studied in homogenous and simple systems, such as isolated cell populations or early development models. Whether it can sensitively be assessed in complex, dynamic systems in vivo remains largely unexplored. In this study, we identify chromatin accessibility changes in a whole organism from embryogenesis to adulthood, using C. more...

Organism:

Caenorhabditis elegans

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13657

10 Samples

Download data: NARROWPEAK

(Submitter supplied) R-loop, a three-stranded RNA/DNA structure, has been linked to induced genome instability and regulated gene expression. To enable precision analysis of R-loops in vivo, we develop an RNase H-based approach, revealing predominant R-loop formation near gene promoters with strong G/C skew and propensity to form G-quadruplex in non-template DNA, corroborating with all biochemically established properties of R-loops. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL16791

25 Samples

Download data: BW

(Submitter supplied) R-loops impact transcription and genome stability and are related to human diseases. Genome-wide R-loop mapping typically uses the S9.6 antibody or inactive RNase H, both requiring a large number of cells with varying results observed depending on the approach applied. Here, we present strand-specific KAS-seq (spKAS-seq) to map R-loops by taking advantage of the presence of a single-stranded DNA (ssDNA) in the triplex structure. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL24676

46 Samples

Download data: BIGWIG