GEO DataSets

(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) 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) 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) 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) We analyzed the genome wide distributions of Brd2 and Brd4 in Th17 cells. We find that Brd2 and Brd4 have distinct genome-wide localization in Th17 cells, further experiments reveal tht Brd2 faciliates TF-complex formation in enhancers, enhancer-promoter interaction while Brd4 enhances transcriptional elongation.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13112

18 Samples

Download data: WIG

(Submitter supplied) We analyzed the ChIP-seq data of Brd2 and Brd4 in Th17 cells. We find that Brd2 and Brd4 have distinct genome-wide deposition in Th17 cells, further experiments reveal tht Brd2 faciliates TF-complex formation in enhancers, enhancer-promoter interaction while Brd4 enhances transcriptional elongation.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9185

10 Samples

Download data: BED, TXT

(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) Long non-coding enhancer RNAs (lnc-eRNAs) are a subset of stable eRNAs identified from the annotated lncRNAs. They might serve as enhancer activity-related therapeutic targets in cancer; however, the epigenetic activation mechanisms and the function of lnc-eRNAs in cancer initiation and progression remain largely unknown.Here, by genome-wide screening we firstly identified a set of lncRNAs as lnc-eRNAs according to the epigenetic signatures of enhancers.To demonstrate the functional roles of lnc-eRNAs, two newly identified lnc-eRNAs, SEELA1 and SEELA2, were chosen for further studies.Further studies showed that SEELA1/2-SERINC2 axis regulated cancer metabolism, such as sphingolipid synthesis, to affect the leukemia progression.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

9 Samples

Download data: XLSX

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

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21290

20 Samples

Download data

(Submitter supplied) Here we report the discovery of ABBV-744, a first in class, highly potent and selective inhibitor of BET family BD2 domains with drug like properties. RNA-seq analysis revealed that ABBV-744 elicited potent inhibition of AR-dependent transcription without causing broad transcription alterations associated with exposure to pan BET inhibitors.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21290

10 Samples

Download data: TXT

(Submitter supplied) Here we report the discovery of ABBV-744, a first in class, highly potent and selective inhibitor of BET family BD2 domains with drug like properties. ChIP-seq analysis revealed that ABBV-744 displaced BRD4 from AR-containing super enhancers and elicited potent inhibition of AR-dependent transcription without causing broad transcription alterations associated with exposure to pan BET inhibitors.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18573

14 Samples

Download data: BW

(Submitter supplied) Here we report the discovery of ABBV-744, a first in class, highly potent and selective inhibitor of BET family BD2 domains with drug like properties. RNA-seq analysis revealed that ABBV-744 elicited potent inhibition of AR-dependent transcription without causing broad transcription alterations associated with exposure to pan BET inhibitors.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21290

10 Samples

Download data: TXT

(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) DNA damage activates a complex signaling network in cells that blocks cell cycle progression, recruits factors involved in DNA repair, and/or triggers programs that control senescence or programmed cell death. Alterations in chromatin structure are known to be important for the initiation and propagation of the DNA damage response, although the molecular details are unclear. We investigated the role of chromatin structure in the DNA damage response by monitoring multiple timedependent checkpoint signaling and response events with a high-content multiplex image-based RNAi screen of chromatin modifying and interacting genes. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL571

4 Samples

Download data: CEL

(Submitter supplied) Purpose: BRD4 is a chromatin reader and transcriptional activator of M/G1 genes.We discovered that BRD4 is a novel histone acetyltransferase that acetylates histones and evicts nucleosomes. Here, investigated genome-wide changes in nucleosome occupancy and transcription caused by BRD4 HAT activity . Method: Human U2OS cells were transfected with either wild type BRD4 (WT), a BRD4 HAT mutant (MT) or a empty vector (NT) in biological duplicates, harvested 18 hrs post transfection and subjected to global MNase-seq and RNA-seq analysis. more...

Organism:

Homo sapiens

Type:

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

Platform:

GPL11154

12 Samples

Download data: RPKM, WIG

(Submitter supplied) During the post-meiotic phase of spermatogenesis, transcription is progressively repressed as the nuclei of haploid spermatids are compacted through a dramatic chromatin reorganization involving hyper-acetylation and replacement of most histones with sperm-specific protamines. Although BRDT has been shown to function in transcription as well as histone removal in post-meiotic spermatids, it is unknown whether other BET family proteins play a role. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19057

9 Samples

Download data: BED, BW

(Submitter supplied) The bromodomain and extra-terminal (BET) protein BRD4 functions as a transcriptional activator and is a therapeutic target for different human cancers. Here, we report a critical link between Polycomb repressive deubiquitinase-BAP1 (PR-DUB) complex and BRD4, which is bridged by the physical interaction between additional sex combs-like protein 3 (ASXL3) in small cell lung cancer (SCLC). We further showed that ASXL3 functions as an adaptor protein, which directly interacts with BRD4-extra-terminal (ET) domain via a novel BRD4 binding motif (BBM), and maintains chromatin occupancy of BRD4 at active enhancers. more...

Organism:

Mus musculus; Homo sapiens

Type:

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

Platforms:

GPL16791 GPL17021

37 Samples

Download data: BW

(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:

GPL11154 GPL16791

94 Samples

Download data: BIGWIG

(Submitter supplied) Cellular senescence is a homeostatic program associated with tumor suppression, wound healing, and certain age related pathologies. Senescent cells display a repressive chromatin configuration thought to stably silence proliferation-promoting genes, while at the same time activate an unusual form of immune surveillance involving a secretory program referred to as the senescence-associated secretory phenotype (SASP). more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

72 Samples

Download data: TXT