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ProteomicsA super-enhancer regulated RNA-binding protein cascade drives pancreatic cancer
Pancreatic ductal adenocarcinoma (PDAC) is a lethal malignancy in need of new therapeutic options. Using an unbiased analysis of super-enhancers (SEs) as sentinels of core genes involved in cell-specific function, we uncover a druggable SE-mediated RNA-binding protein (RBP) cascade that supports PDA...
ORGANISM(S): Mus musculus (Mouse) 
2023-06-15 | PXD030423 | Pride
Prmt1 Rna-binding protein Pancreatic cancer Super-enhancers Tumor growth 
GenomicsBcl6 and NFkB cistromes mediate opposing reulation of the innate immune response
Here, using ChIP-seq, we define the NF-κB cistrome which is comprised of 31,070 cis-acting binding sites responsive to LPS-induced signaling. In addition, we demonstrate that the transcriptional repressor B-cell lymphoma 6 (Bcl-6) regulates nearly a third of the Tlr4-regulated transcriptome and tha...
ORGANISM(S): Mus musculus 
2010-11-24 | E-GEOD-16723 | biostudies-arrayexpress
TranscriptomicsCryptochromes mediate rhythmic repression of the glucocorticoid receptor
The circadian transcriptional repressors cryptochromes 1 (Cry1) and 2 (Cry2) interact with the C-terminus of the glucocorticoid receptor (GR) and are required for transrepression in response to the synthetic GR ligand dexamethasone (Dex) in mouse embryonic fibroblasts. Dex induction of many genes w...
ORGANISM(S): Mus musculus 
2011-12-22 | E-GEOD-24469 | biostudies-arrayexpress
GenomicsCreation of an anti-inflammatory GR cistrome by TLR4 signaling
An unresolved molecular paradox is how the glucocorticoid receptor (GR) activates some genes while potently repressing others. We carried out genome-wide localization and expression profiling experiments in primary bone marrow-derived mouse macrophages treated with Dexamethasone in the presence or a...
ORGANISM(S): Mus musculus 
2012-12-04 | E-GEOD-31796 | biostudies-arrayexpress
GenomicsSuper-Enhancer-mediated Control of Liver Fibrosis by BET Bromodomain Proteins
Here, we investigate the role of enhancers in myofibroblasts, a cell type that dominates the pathogenesis and progression of tissue fibrosis. We reveal that bromodomain and extra-terminal family members (BETs), an important group of epigenetic readers, are critical for super-enhancer-mediated pro-fi...
ORGANISM(S): Homo sapiens 
2015-12-11 | E-GEOD-58680 | biostudies-arrayexpress
TranscriptomicsExpression data from quadriceps muscle of WT and ERRgamma transgenic mice
We show that the orphan nuclear receptor ERRg is expressed at high levels in type I muscle and when transgenically expressed in anaerobic type II muscles (ERRGO mice) or cultured cells, powerfully regulates VEGF expression, angiogenesis and vascular supply in absence of exercise. ERRGO mice show in...
ORGANISM(S): Mus musculus 
2011-09-18 | E-GEOD-22086 | biostudies-arrayexpress
GenomicsA master cistromic circuit governing hepatic fibrogenesis [ChIP-seq]
Liver fibrosis is a reversible wound-healing response to liver injury and hepatic stellate cells (HSCs) are central cellular players that mediate hepatic fibrogenesis. However, the molecular mechanisms that govern this process remain unclear. Here, we reveal a novel cistromic circuit in HSCs compris...
ORGANISM(S): Homo sapiens 
2013-04-29 | E-GEOD-38103 | biostudies-arrayexpress
GenomicsGenome-wide location analysis of SMRT and NCoR in wild-type and Bcl6 knockout macrophages
Using ChIP-seq, we reveal the SMRT and NCoR co-repressor cistromes, which each consist of over 30,000 half-shared binding sites. Moreover, we identify Bcl6-bound sub-cistromes for each co-repressor, which are strongly concentrated on NF-κB-driven inflammatory and tissue remodeling genes. These res...
ORGANISM(S): Mus musculus 
2012-03-29 | E-GEOD-27033 | biostudies-arrayexpress
GenomicsIntegral roles for Rev-erb alpha and Rev-erb beta in the circadian clock function [ChIP_seq]
The circadian clock acts at the genomic level to coordinate internal behavioral and physiologic rhythms via the CLOCK-BMAL transcriptional heterodimer. Although the nuclear receptors REV-ERBα and β have been proposed to contribute to clock function, their precise roles and importance remain unresol...
ORGANISM(S): Mus musculus 
2012-03-28 | E-GEOD-34019 | biostudies-arrayexpress
TranscriptomicsIntegral roles for Rev-erb alpha and Rev-erb beta in the circadian clock function [Expression array]
The circadian clock acts at the genomic level to coordinate internal behavioral and physiologic rhythms via the CLOCK-BMAL transcriptional heterodimer. Although the nuclear receptors REV-ERB? and ? have been proposed to contribute to clock function, their precise roles and importance remain unresol...
ORGANISM(S): Mus musculus 
2012-03-28 | E-GEOD-34018 | biostudies-arrayexpress
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