GEO DataSets

(Submitter supplied) To study the role of the bromodomain (BD) in BRD4-dependent gene expression, we compared the function of wild type BRD4 and a mutant BRD4-mBD, which carries a point mutation in each of the two BDs. We first knocked down endogenous BRD4 by shRNA (shBRD4) and then stably reconstituted the cells with shBRD4-resistant YFP-BRD4 (wild type or mBD mutant). Following BRD4 reconstitution, the degree of recovery in gene expression was analyzed by Affymetrix Mouse Exon 1.0 ST array. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6096

8 Samples

Download data: CEL, CHP

(Submitter supplied) In serum-starved and re-fed mouse fibroblast, nascent RNA-seq analysis showed that the BET inhibitor JQ1 antagonized a process regulating PIC formation and a downstream process involved in progressive elongation. To specifically address the role of BRD4 and its interactions with acetylated histones and P-TEFb, YFP-tagged BRD4 proteins (wild type and mutant BRD4) were stably expressed in cells, endogenous BRD4 of which was knocked down by shRNA (shBRD4). more...

Organism:

Mus musculus

Type:

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

Platform:

GPL13112

41 Samples

Download data: BEDGRAPH, BW

(Submitter supplied) Transcriptional elongation by RNA polymerase II (Pol II) is regulated by positive transcription elongation factor b (P-TEFb) in association with Bromodomain-containing protein 4 (BRD4). We used genome-wide chromatin immunoprecipitation sequencing in primary human CD4+ T cells to reveal that BRD4 co-localizes with Ser2-phosphorylated Pol II (Pol II Ser2) at both enhancers and promoters of active genes. more...

Organism:

Homo sapiens

Type:

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

Platforms:

GPL10999 GPL11154

15 Samples

Download data: BED, WIG

(Submitter supplied) In this study, we provide a previously unrecognized convergence between eRNAs and histone acetylation in regulating the chromatin interactions and transcription functions of BRD4.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20301

2 Samples

Download data: BIGWIG

(Submitter supplied) We establish a mechanism by which chronic TNF-a signaling orchestrates a functional interplay between mutant p53 and NFkB that underlies altered patterns of cancer promoting gene expression.

Organism:

Homo sapiens

Type:

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

Platform:

GPL20301

17 Samples

Download data: BIGWIG, CSV

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

Organism:

Homo sapiens

Type:

Other; Genome binding/occupancy profiling by high throughput sequencing

4 related Platforms

56 Samples

Download data: BEDGRAPH, BW

(Submitter supplied) In this study, we reveal that BRD4 underlies a general 5'-elongation checkpoint that primes transcribing RNA polymerase II for 3'-RNA processing and transcription termination. BRD4-specific degradation impairs Pol II pause release, induces massive readthrough transcription, and RNA cleavage defects. Acute loss of BRD4 disrupts the recruitment of 3'-RNA processing factors.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24676

34 Samples

Download data: BW

(Submitter supplied) In this study, we reveal that BRD4 underlies a general 5'-elongation checkpoint that primes transcribing RNA polymerase II for 3'-RNA processing and transcription termination. BRD4-specific degradation impairs Pol II pause release, induces massive readthrough transcription, and RNA cleavage defects. Acute loss of BRD4 disrupts the recruitment of 3'-RNA processing factors.

Organism:

Homo sapiens

Type:

Other

Platform:

GPL24106

4 Samples

Download data: BW

(Submitter supplied) In this study, we reveal that BRD4 underlies a general 5'-elongation checkpoint that primes transcribing RNA polymerase II for 3'-RNA processing and transcription termination. BRD4-specific degradation impairs Pol II pause release, induces massive readthrough transcription, and RNA cleavage defects. Acute loss of BRD4 disrupts the recruitment of 3'-RNA processing factors.

Organism:

Homo sapiens

Type:

Other

Platforms:

GPL18573 GPL20301 GPL24676

18 Samples

Download data: BEDGRAPH

(Submitter supplied) The BET family protein BRD4, which forms the CDK9-containing BRD4-PTEFb complex, is considered to be a master regulator of RNA polymerase II (Pol II) pause release. Because its tandem bromodomains interact with acetylated histone lysine residues, it has long been thought that BRD4 requires these bromodomains for its recruitment to chromatin and transcriptional regulatory function. Here, using rapid depletion and genetic complementation with domain deletion mutants, we demonstrate that BRD4 bromodomains are dispensable for Pol II pause release. more...

Organism:

Homo sapiens

Type:

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

Platform:

GPL24676

122 Samples

Download data: BW, TSV, XLSX

(Submitter supplied) The transition from transcription initiation to elongation is a key regulatory step in gene expression, which requires RNA polymerase II (Pol II) to escape promoter proximal pausing on chromatin. While elongation factors promote pause release leading to transcription elongation, the role of epigenetic modifications during this critical transition step is poorly understood. Two histone marks on histone H3, lysine 4 trimethylation (H3K4me3) and lysine 9 acetylation (H3K9ac), co-localize on active gene promoters and are associated with active transcription. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11154

5 Samples

Download data: BW

(Submitter supplied) To test whether Brd4 and SEC co-regulate the release of promoter-proximally paused Pol II, we performed Pol II ChIP-Seq to analyze the effect of depletion of Brd4 or SEC on HMBA-induced pause release in HCT116 cells.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL16791

6 Samples

Download data: BED

(Submitter supplied) Distal enhancers characterized by H3K4me1 mark play critical roles in developmental and transcriptional programs. However, potential roles of specific distal regulatory elements in regulating RNA Polymerase II (Pol II) promoter-proximal pause release remain poorly investigated. Here we report that a unique cohort of jumonji C domain-containing protein 6 (JMJD6) and bromodomain-containing protein 4 (Brd4) co-bound distal enhancers, termed anti-pause enhancers (A-PEs), regulate promoter-proximal pause release of a large subset of transcription units via long-range interactions. more...

Organism:

Homo sapiens

Type:

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

Platforms:

GPL9115 GPL11154

40 Samples

Download data: BIGWIG

(Submitter supplied) We identified a chromatin displacement signature for the bromodomain proteins BRD2, BRD3 and BRD4 at TSS following treatment with I-BET152, an inhibitor of BET proteins. By integrating ChIP-seq, RNA-seq and Chem-seq data, we correlated alteration of the BRD4 signature at TSS with strong downregulation of gene expression which will facilitate identification of markers of sensitivity and resistance to drug.

Organism:

Homo sapiens

Type:

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

Platform:

GPL11154

88 Samples

Download data: BED, BW, TXT

(Submitter supplied) Twist is a key EMT inducer, expression of Twist will induce EMT in HMLE and breast tumor T47D cells By expressing Twist in HMLE and T47D cells, which lack the expression of Twist, will identify the genes regulated by Twist

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6244

8 Samples

Download data: CEL, CHP

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

Organism:

Homo sapiens

Type:

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

Platforms:

GPL18573 GPL10999

78 Samples

Download data: BEDGRAPH, WIG

(Submitter supplied) The MYC transcription factor is an unstable protein and its turnover is controlled by the ubiquitin system. Ubiquitination enhances MYC-dependent transactivation, but the underlying mechanism remains unresolved. Here we show that proteasomal turnover of MYC is dispensable for recruitment of RNA polymerase II (RNAPII), but is required to promote transcriptional elongation at MYC target genes. Degradation of MYC stimulates histone acetylation and recruitment of BRD4 and P-TEFb to target promoters, leading to phosphorylation of RNAPII CTD and the release of elongating RNAPII. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL10999 GPL18573

31 Samples

Download data: BEDGRAPH, WIG

(Submitter supplied) The MYC transcription factor is an unstable protein and its turnover is controlled by the ubiquitin system. Ubiquitination enhances MYC-dependent transactivation, but the underlying mechanism remains unresolved. Here we show that proteasomal turnover of MYC is dispensable for recruitment of RNA polymerase II (RNAPII), but is required to promote transcriptional elongation at MYC target genes. Degradation of MYC stimulates histone acetylation and recruitment of BRD4 and P-TEFb to target promoters, leading to phosphorylation of RNAPII CTD and the release of elongating RNAPII. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL18573 GPL10999

47 Samples

Download data: BEDGRAPH, CSV

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

Organism:

Mus musculus

Type:

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

Platforms:

GPL17021 GPL19057

46 Samples

Download data: BW

(Submitter supplied) Transcriptional regulation in eukaryotes commonly occurs at promoter-proximal regions wherein transcriptionally engaged RNA Polymerase II (Pol II) pauses before proceeding towards productive elongation. The roles of chromatin in this process remains poorly understood. Here, we demonstrate that the histone deacetylase SIRT6 regulates transcription elongation by binding to Pol II and anchoring the Negative ELongation Factor NELF, thereby preventing the release of Pol II towards elongation. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL19057

8 Samples

Download data: BW