Study / S4ZCKILX92016-08-25

Direct GR Binding Sites Potentiate Clusters of TF Binding across the Human Genome

Christopher M. Vockley, Anthony M. D'Ippolito, Ian C. McDowell, William H. Majoros, Alexias Safi et al.

Read publication Raw data (33)Download all raw data (ZIP)

About this study

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.

Full author list & citation

Christopher M. Vockley, Anthony M. D'Ippolito, Ian C. McDowell, William H. Majoros, Alexias Safi, Lingyun Song, Gregory E. Crawford, Timothy E. Reddy. Direct GR Binding Sites Potentiate Clusters of TF Binding across the Human Genome. 2016-08-25. https://doi.org/10.1016/j.cell.2016.07.049

Experiments 2

E1S5BZAN3

BAC-based STARR-seq validation of GR-bound regions

Six human BACs containing previously identified DEX-responsive genes were tagmented into an episomal STARR-seq library and assayed in A549 cells after DEX or ethanol treatment. The table is the publication's base-resolution sliding-window DEX-versus-ethanol significance track across the BAC-covered loci.

Standard STARR-seqHumanhg19

Explore data

E769G8PA5

Genome-scale GR ChIP-enriched STARR-seq reporter assay

A549 cells were transfected with an episomal STARR-seq library made from GR ChIP-seq fragments and treated with 100 nM dexamethasone or 0.02% ethanol vehicle for 3 h. The table contains the site-level DESeq2 reporter-RNA contrast for the 10,963 GR binding-site subpeaks that passed the publication's statistical-power filter.

Standard STARR-seqHumanhg19

Explore data

Raw source data 33 files

Original supplemental and deposited inputs retained for this study. Download files individually or together as a ZIP; nested folders are preserved. Source reuse terms apply, and sequencing reads may be omitted.