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| Status |
Public on Aug 25, 2016 |
| Title |
Direct GR binding sites potentiate clusters of TF binding across the human genome [5] |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| 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.
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| 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.
In dataset [5], the files contain RNA-seq from GR-ChIP-reporters that were transfected into A549 cells and treated with DEX or EtOH.
[5] contains the reporter assay specific RNA-seq from plasmids described in [4].
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| Contributor(s) |
Vockley CM, D'Ippolito AM, McDowell IC, Majoros WH, Safi A, Song L, Crawford GE, Reddy TE |
| Citation missing |
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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
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| Organization name |
Duke University
|
| Street address |
101 science drive rm 2193
|
| City |
Durham |
| State/province |
NC |
| ZIP/Postal code |
27708 |
| Country |
USA |
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| Platforms (1) |
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| Samples (6)
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| This SubSeries is part of SuperSeries: |
| GSE79432 |
Direct GR binding sites potentiate clusters of TF binding across the human genome |
|
| Relations |
| BioProject |
PRJNA315840 |
| SRA |
SRP072107 |
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