GEO DataSets

(Submitter supplied) The transition of RNA polymerase II (Pol II) from initiation to productive elongation is a central, regulated step in metazoan gene expression. At many genes, Pol II pauses stably in early elongation, remaining engaged with the 25-60 nucleotide-long nascent RNA for many minutes while awaiting signals for release into the gene body. However, a number of genes display highly unstable promoter Pol II, suggesting that paused polymerase terminates transcription at these promoters and releases a short, non-functional RNA. more...

Organism:

Drosophila melanogaster

Type:

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

Platform:

GPL19132

16 Samples

Download data: BEDGRAPH, BW

(Submitter supplied) Efficient release of promoter-proximally paused Pol II into productive elongation is essential for gene expression. Recently, we reported that the Integrator complex can bind paused Pol II and drive premature transcription termination, potently attenuating the activity of target genes. Premature termination requires RNA cleavage by the endonuclease subunit of Integrator, but the roles of other Integrator subunits in gene regulation have yet to be elucidated. more...

Organism:

Homo sapiens; Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL19132 GPL20301

32 Samples

Download data: TXT

(Submitter supplied) Transcription activation involves RNA polymerase II (Pol II) recruitment and release from the promoter into productive elongation, but how specific chromatin regulators control these steps is unclear. Here we identify a novel activity of the histone acetyltransferase p300/CBP in regulating promoter-proximal paused Pol II. We find that Drosophila CBP (nejire) inhibition impedes transcription through the +1 nucleosome leading to accumulation of Pol II at this position on all expressed genes. more...

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17275

12 Samples

Download data: SGR

(Submitter supplied) TFIIB chromatin binding is drastically reduced genome-wide after 10 min of CBP (also known as nejire) inhibition.

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17275

8 Samples

Download data: SGR

(Submitter supplied) Nucleosome position does not change after 10 min of CBP (also known as nejire) inhibition.

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17275

4 Samples

Download data: SGR

(Submitter supplied) Transcription activation involves RNA polymerase II (Pol II) recruitment and release from the promoter into productive elongation, but how specific chromatin regulators control these steps is not fully understood. Here we identify a novel activity of the co-regulator and histone acetyltransferase p300/CBP in positioning promoter-proximal paused Pol II. We find that CBP inhibition impedes transcription through the +1 nucleosome, causing “dribbling” of Pol II from the canonical pause site genome-wide. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL19132

2 Samples

Download data: BIGWIG

(Submitter supplied) Metazoan gene expression is often regulated after the recruitment of RNA polymerase II (Pol II) to promoters, through the controlled release of promoter-proximally paused Pol II into productive RNA synthesis. Despite the prevalence of paused Pol II, very little is known about the dynamics of these early elongation complexes or the fate of short transcription start site-associated (tss) RNAs they produce. more...

Organism:

Drosophila melanogaster

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL11203

9 Samples

Download data: BEDGRAPH

(Submitter supplied) Transcription by RNA polymerase II (RNAPII) is pervasive in the human genome. However, the mechanisms controlling transcription at promoters and enhancers remain enigmatic. Here, we demonstrate that Integrator subunit 11 (INTS11), the catalytic subunit of the Integrator complex, regulates transcription at these loci through its endonuclease activity. Promoters of genes require INTS11 to cleave nascent transcripts associated with paused RNAPII and induce their premature termination in the proximity of the +1 nucleosome. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL18573

16 Samples

Download data: BW

(Submitter supplied) Transcription by RNA polymerase II (RNAPII) is pervasive in the human genome. However, the mechanisms controlling transcription at promoters and enhancers remain enigmatic. Here, we demonstrate that Integrator subunit 11 (INTS11), the catalytic subunit of the Integrator complex, regulates transcription at these loci through its endonuclease activity. Promoters of genes require INTS11 to cleave nascent transcripts associated with paused RNAPII and induce their premature termination in the proximity of the +1 nucleosome. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL18573

70 Samples

Download data: BED, BW, TXT

(Submitter supplied) Transcription by RNA polymerase II (Pol II) is coupled to pre-mRNA splicing, but the underlying mechanisms remain poorly understood. Co-transcriptional splicing requires assembly of a functional spliceosome on nascent pre-mRNA, but whether and how this influences Pol II transcription remains unclear. Here we show that inhibition of pre-mRNA branch site recognition by the spliceosome component U2 snRNP leads to a widespread and strong decrease in new RNA synthesis in human cells. more...

Organism:

Homo sapiens

Type:

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

Platforms:

GPL18573 GPL21697

48 Samples

Download data: BW, GTF

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

Organism:

Drosophila melanogaster

Type:

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

Platforms:

GPL13304 GPL21306

42 Samples

Download data: TXT

(Submitter supplied) We sought to determine the genomic binding profile of the Drosophila Hox protein Ubx in a homogenous cell system. S2-DRSC cells that have no Hox expression were stably transfected with HA-tagged Ubx under the control of a metallothionein promoter. Upon Ubx expression, we identified high enrichment of Ubx at a large number transcription start sites that colocalises with the GAGA and M1BP.

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13304

3 Samples

Download data: BED

(Submitter supplied) We sought to determine the genes regulated by the Drosophila Hox protein AbdA in a homogenous cell system. S2-DRSC cells that have no Hox expression were stably transfected with HA-tagged AbdA under the control of a metallothionein promoter.

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13304

6 Samples

Download data: TXT, XLS

(Submitter supplied) We sought to determine the genomic binding profile of the Drosophila Hox protein AbdA in a homogenous cell system. S2-DRSC cells that have no Hox expression were stably transfected with HA-tagged AbdA under the control of a metallothionein promoter. Upon AbdA expression, we identified high enrichment of AbdA at a large number transcription start sites that colocalises with the GAGA and M1BP. Genes targeted by GAGA and M1BP contain paused RNA polymerase II and show enrichment of PcG proteins. more...

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL13304 GPL21306

33 Samples

Download data: BED, BIGWIG

(Submitter supplied) The control of promoter-proximal pausing and the release of RNA polymerase II (RNA Pol II) is a widely used mechanism for regulating gene expression in metazoans, especially for genes that respond to environmental and developmental cues. Here, we identify Pol II associated Factor 1 (PAF1) as a major regulator of promoter-proximal pausing. Knockdown of PAF1 leads to increased release of paused Pol II into gene bodies at thousands of genes. more...

Organism:

Homo sapiens; Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing; Other

Platforms:

GPL18573 GPL11154 GPL19132

61 Samples

Download data: BW

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

Organism:

Drosophila melanogaster

Type:

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

Platforms:

GPL13304 GPL6629

14 Samples

Download data: BAR, BED, BEDGRAPH, CEL

(Submitter supplied) Cohesin is a well-known mediator of sister chromatid cohesion, but it also influences gene expression and development. These non-canonical roles of cohesin are not well understood, but are vital: gene expression and development are altered by modest changes in cohesin function that do not disrupt chromatid cohesion. To clarify cohesin’s roles in transcription, we measured how cohesin controls RNA polymerase II (Pol II) activity by genome-wide chromatin immunoprecipitation and precision global run-on sequencing. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13304

6 Samples

Download data: BEDGRAPH

(Submitter supplied) Cohesin is a well-known mediator of sister chromatid cohesion, but it also influences gene expression and development. These non-canonical roles of cohesin are not well understood, but are vital: gene expression and development are altered by modest changes in cohesin function that do not disrupt chromatid cohesion. To clarify cohesin’s roles in transcription, we measured how cohesin controls RNA polymerase II (Pol II) activity by genome-wide chromatin immunoprecipitation and precision global run-on sequencing. more...

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL6629

8 Samples

Download data: BAR, BED, CEL

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below. FACT (Facilitates Chromatin Transcription) is an evolutionarily conserved histone chaperone that was initially identified as an activity capable of promoting RNA polymerase II transcription through nucleosomes in vitro. In this report, we describe a global analysis of FACT function in Pol II transcription in Drosophila. We present evidence that loss of FACT has a dramatic impact on Pol II elongation-coupled processes including H3K4 and H3K36 methylation, consistent with a role for FACT in coordinating histone modification and chromatin architecture during Pol II transcription. more...

Organism:

Drosophila melanogaster

Type:

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

Platforms:

GPL19132 GPL17275

162 Samples

Download data: BW, TAB

(Submitter supplied) The highly conserved histone chaperone FACT (Facilitates Chromatin Transcription) is thought to contribute to the disassembly and reassembly of nucleosomes in the wake of RNA Polymerase II (Pol II) passage through chromatin. However, FACT’s roles in chromatin biology and transcriptional regulation in vivo in higher eukaryotes are not well understood. Here, we report that depletion of FACT leads to a reduction in the duration of promoter-proximal pausing by Pol II in Drosophila S2 cells. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17275

10 Samples

Download data: TAB, TSV