GEO DataSets

(Submitter supplied) Transcript elongation by RNA polymerase II (RNAPII) is accompanied by conserved patterns of histone modification within transcribed regions, but it remains uncertain how these modifications influence, or are influenced by, properties of the elongation complex. Here we establish an intimate link between Cdk9, the kinase component of positive transcription elongation factor b (P-TEFb), and mono-ubiquitylation of histone H2B (H2Bub1), in the fission yeast Schizosaccharomyces pombe. more...

Organism:

Schizosaccharomyces pombe

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL16218

6 Samples

Download data: GPR, TIFF

(Submitter supplied) Histone H2B mono-ubiquitylation (H2Bub1) and phosphorylation of elongation factor Spt5 by cyclin-dependent kinase 9 (Cdk9) occur during transcription by RNA polymerase II (RNAPII), and are mutually dependent in fission yeast. How Cdk9 activity and H2Bub1 cooperate to regulate the expression of individual genes remains unclear. Here we show Cdk9 inhibition or H2Bub1 loss induces intragenic antisense transcription of distinct gene subsets; ablation of both pathways derepresses antisense transcription of over half the genome. more...

Organism:

Schizosaccharomyces pombe

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL20584 GPL13988

24 Samples

Download data: BIGWIG

(Submitter supplied) The end of the RNA polymerase II (Pol II) transcription cycle is strictly regulated to ensure proper mRNA maturation and prevent interference between neighboring genes. Pol II slowing downstream of the cleavage and polyadenylation signal (CPS) leads to recruitment of cleavage and polyadenylation factors and termination, but how this chain of events is initiated remains unclear. In a chemical-genetic screen we identified protein phosphatase 1 (PP1) isoforms as substrates of human positive transcription elongation factor b (P-TEFb), the cyclin-dependent kinase 9 (Cdk9)-cyclin T1 complex. more...

Organism:

Schizosaccharomyces pombe

Type:

Other; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL20584 GPL13988

52 Samples

Download data: BEDGRAPH, BIGWIG, BW

(Submitter supplied) ChIP-chip of histone variants and modifications in A. thaliana WT and various mutants

Organism:

Schizosaccharomyces pombe

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL16218

26 Samples

Download data: GPR, TIFF

(Submitter supplied) Many proteins associate with elongating RNA polymerase II (RNAPII), although the functions of most of them are still not well understood. Spt5 is an essential transcription elongation factor that binds directly to RNA polymerase and is conserved in prokaryotes, archaea, and eukaryotes1. In eukaryotes, evidence suggests that Spt5 functions in transcription elongation by both RNA polymerases I and II, mRNA capping, mRNA splicing, and mRNA 3’ end formation2. more...

Organism:

Schizosaccharomyces pombe

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20584

32 Samples

Download data: BEDGRAPH

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

Organism:

Schizosaccharomyces pombe

Type:

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

Platforms:

GPL20584 GPL13988 GPL17225

70 Samples

Download data: BEDGRAPH, BIGWIG, TXT, WIG

(Submitter supplied) Many proteins associate with elongating RNA polymerase II (RNAPII), although the functions of most of them are still not well understood. Spt5 is an essential transcription elongation factor that binds directly to RNA polymerase and is conserved in prokaryotes, archaea, and eukaryotes1. In eukaryotes, evidence suggests that Spt5 functions in transcription elongation by both RNA polymerases I and II, mRNA capping, mRNA splicing, and mRNA 3’ end formation2. more...

Organism:

Schizosaccharomyces pombe

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17225

6 Samples

Download data: BIGWIG, TXT

(Submitter supplied) Many proteins associate with elongating RNA polymerase II (RNAPII), although the functions of most of them are still not well understood. Spt5 is an essential transcription elongation factor that binds directly to RNA polymerase and is conserved in prokaryotes, archaea, and eukaryotes1. In eukaryotes, evidence suggests that Spt5 functions in transcription elongation by both RNA polymerases I and II, mRNA capping, mRNA splicing, and mRNA 3’ end formation2. more...

Organism:

Schizosaccharomyces pombe

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17225

16 Samples

Download data: BEDGRAPH

(Submitter supplied) Many proteins associate with elongating RNA polymerase II (RNAPII), although the functions of most of them are still not well understood. Spt5 is an essential transcription elongation factor that binds directly to RNA polymerase and is conserved in prokaryotes, archaea, and eukaryotes1. In eukaryotes, evidence suggests that Spt5 functions in transcription elongation by both RNA polymerases I and II, mRNA capping, mRNA splicing, and mRNA 3’ end formation2. more...

Organism:

Schizosaccharomyces pombe

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17225

12 Samples

Download data: WIG

(Submitter supplied) Many proteins associate with elongating RNA polymerase II (RNAPII), although the functions of most of them are still not well understood. Spt5 is an essential transcription elongation factor that binds directly to RNA polymerase and is conserved in prokaryotes, archaea, and eukaryotes1. In eukaryotes, evidence suggests that Spt5 functions in transcription elongation by both RNA polymerases I and II, mRNA capping, mRNA splicing, and mRNA 3’ end formation2. more...

Organism:

Schizosaccharomyces pombe

Type:

Other; Expression profiling by high throughput sequencing

Platform:

GPL13988

4 Samples

Download data: WIG

(Submitter supplied) Post-translational modifications of the transcription elongation complex provide mechanisms to fine-tune gene expression, yet their specific impacts on RNA polymerase II regulation remain difficult to ascertain. Here, in Schizosaccharomyces pombe, we examine the role of Cdk9, and related Mcs6/Cdk7 and Lsk1/Cdk12 kinases, on transcription at base-pair resolution with Precision Run-On sequencing (PRO-seq). more...

Organism:

Schizosaccharomyces pombe

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL20584

40 Samples

Download data: BW

(Submitter supplied) Using wild type and Ash1l ∆SET mutant embryonic stem cells, against a prevalent notion, here we report di-,tri-methylation of histone H3 Lys36 occur independently of ongoing transcription. Ash1l ∆SET mutant shows the impaired methylation levels in broad range of genome. Intriguingly, data implicate that a binding of retinoic acid receptor to a certain genomic region promotes installation of the tri-methylation in the retinoic acid receptor-associated gene independent of its ongoing transcription.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL15103

10 Samples

Download data: WIG

(Submitter supplied) Using wild type and Ash1l deltaSET mutant embryonic stem cells, here we report differences of gene expression pattern under undifferentiated state and differentiated state. Interestingly, gene expression changes are frequently observed in a subset of gene group that is regulated by Polycomb group proteins.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15103

4 Samples

Download data: FPKM_TRACKING

(Submitter supplied) The histone chaperone FACT and histone H2B ubiquitination (H2Bub) facilitate RNA Polymerase II passage through chromatin. It remains unknown to what extent they cooperate in vivo. Here, we used genome-wide, genetic, biochemical and microscopic approaches to dissect their interplay in the fission yeast Schizosaccharomyces pombe. We show that FACT and H2Bub repress antisense transcripts near the 5’ end and inside gene bodies, respectively. more...

Organism:

Schizosaccharomyces pombe

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13988

44 Samples

Download data: BEDGRAPH

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

Organism:

Schizosaccharomyces pombe

Type:

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

Platform:

GPL13988

84 Samples

Download data: BEDGRAPH, BW

(Submitter supplied) The histone chaperone FACT and histone H2B ubiquitination (H2Bub) facilitate RNA Polymerase II passage through chromatin. It remains unknown to what extent they cooperate in vivo. Here, we used genome-wide, genetic, biochemical and microscopic approaches to dissect their interplay in the fission yeast Schizosaccharomyces pombe. We show that FACT and H2Bub repress antisense transcripts near the 5’ end and inside gene bodies, respectively. more...

Organism:

Schizosaccharomyces pombe

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13988

32 Samples

Download data: BW

(Submitter supplied) The histone chaperone FACT and histone H2B ubiquitination (H2Bub) facilitate RNA Polymerase II passage through chromatin. It remains unknown to what extent they cooperate in vivo. Here, we used genome-wide, genetic, biochemical and microscopic approaches to dissect their interplay in the fission yeast Schizosaccharomyces pombe. We show that FACT and H2Bub repress antisense transcripts near the 5’ end and inside gene bodies, respectively. more...

Organism:

Schizosaccharomyces pombe

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13988

8 Samples

Download data: BW

(Submitter supplied) A hallmark of genes transcribed by RNA polymerase II (RNApII) is a "gradient" of histone H3 lysine 4 (H3K4) methylation. Various factors differentially bind to H3K4me3 near promoters, H3K4me2 just downstream, and H3K4me1 further downstream to modulate gene expression. Set1/COMPASS, the single S. cerevisiae H3K4 methyltransferase, binds transcribing RNApII, but COMPASS may also be allosterically regulated by specific subunits and histone H2B ubiquitylation. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13821

99 Samples

Download data: BEDGRAPH

(Submitter supplied) Purpose: The ultimate goal of this study is the identification of transcription elongation-related chromatin remodeler and its in vivo mechanism in fission yeast through Next-generation sequencing (NGS) based ChIP-seq technique. Methods: Every ChIP-seq cells were grown up to mid-log phase and harvested after final 1% formaldehyde fixation and 125mM glycine quencing. Cells were harvested by centrifugation at 4 Celcius degrees and the cell pellets were washed by 15mL of pH7.5 TBS buffer per a conical tube. more...

Organism:

Schizosaccharomyces pombe

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17225

123 Samples

Download data: BW

(Submitter supplied) The Pol II transcription cycle is ordered by CDKs and phosphatases. In fission yeast, Cdk9 phosphorylates carboxy-terminal repeats (CTRs) of Spt5 while inhibiting PP1 during elongation. Transcription past the cleavage and polyadenylation signal (CPS) coincides with PP1-dependent Spt5 dephosphorylation and leads to Pol II pausing with phosphorylated CTD-Ser2 (pSer2). Here we show this switch is conserved in humans: Cdk9 inhibition decreases phosphorylation of both PP1g and Spt5-Thr806 (pThr806), and induces pSer2 upstream of the CPS, whereas PP1 depletion increases pThr806. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18573

22 Samples

Download data: BIGWIG