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Series GSE79431 Query DataSets for GSE79431
Status Public on Aug 25, 2016
Title Direct GR binding sites potentiate clusters of TF binding across the human genome [8]
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary The glucocorticoid receptor (GR) binds the human genome at >10,000 sites, but only regulates the expression of hundreds of genes. To determine the functional effect of each site, we measured the glucocorticoid (GC) responsive activity of nearly all GR binding sites (GBSs) captured using chromatin immunoprecipitation (ChIP) in A549 cells. 13% of GBSs assayed had GC-induced activity. The responsive sites were defined by direct GR binding via a GC response element (GRE) and exclusively increased reporter- gene expression. Meanwhile, most GBSs lacked GC-induced reporter activity. The non-responsive sites had epigenetic features of steady state enhancers and clustered around direct GBSs. Together, our data support a model in which clusters of GBSs observed with ChIP-seq reflect interactions between direct and tethered GBSs over tens of kilobases. We further show that those interactions can synergistically modulate the activity of direct GBSs, and may therefore play a major role in driving gene activation in response to GCs.
 
Overall design Glucoroticoid receptor binding site chip-seq libraries were cloned into STARR-seq for massively parallel functional analysis. The results were confirmed by ChIP-Exo performed on the GR in A549 cells treated with 100 nM dexamethasone for one hour.
This dataset [8] contains ChIP-seq data for A549 cells treated with DEX or EtOH for 3 hours.
 
Contributor(s) Vockley CM, D'Ippolito AM, McDowell IC, Majoros WH, Safi A, Song L, Crawford  GE, Reddy TE
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Submission date Mar 21, 2016
Last update date May 15, 2019
Contact name Christopher Vockley
E-mail(s) christopher.vockley@gmail.com
Organization name Duke University
Street address 101 science drive rm 2193
City Durham
State/province NC
ZIP/Postal code 27708
Country USA
 
Platforms (1)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Samples (4)
GSM2095218 ChIP_DEX_rep1
GSM2095219 ChIP_DEX_rep2
GSM2095220 ChIP_EtOH_Rep1
This SubSeries is part of SuperSeries:
GSE79432 Direct GR binding sites potentiate clusters of TF binding across the human genome
Relations
BioProject PRJNA315837
SRA SRP072113

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE79431_RAW.tar 400.0 Kb (http)(custom) TAR (of BED)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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