title: Direct GR Binding Sites Potentiate Clusters of TF Binding across the Human Genome.
abstract: 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.
authors: Department of Cell Biology, Duke University, Durham, NC 27708, USA; Center for Genomic & Computational Biology, Duke University, Durham, NC 27708, USA.
authors: Christopher M
authors: CM
authors: Vockley
authors: Center for Genomic & Computational Biology, Duke University, Durham, NC 27708, USA; University Program in Genetics & Genomics, Duke University, Durham, NC 27708, USA.
authors: Anthony M
authors: AM
authors: D'Ippolito
authors: Center for Genomic & Computational Biology, Duke University, Durham, NC 27708, USA; Program in Computational Biology & Bioinformatics, Duke University, Durham, NC 27708, USA.
authors: Ian C
authors: IC
authors: McDowell
authors: Center for Genomic & Computational Biology, Duke University, Durham, NC 27708, USA; Program in Computational Biology & Bioinformatics, Duke University, Durham, NC 27708, USA.
authors: William H
authors: WH
authors: Majoros
authors: Center for Genomic & Computational Biology, Duke University, Durham, NC 27708, USA; Division of Medical Genetics, Department of Pediatrics, Duke University, Durham, NC 27708, USA.
authors: Alexias
authors: A
authors: Safi
authors: Center for Genomic & Computational Biology, Duke University, Durham, NC 27708, USA; Division of Medical Genetics, Department of Pediatrics, Duke University, Durham, NC 27708, USA.
authors: Lingyun
authors: L
authors: Song
authors: Center for Genomic & Computational Biology, Duke University, Durham, NC 27708, USA; Division of Medical Genetics, Department of Pediatrics, Duke University, Durham, NC 27708, USA.
authors: Gregory E
authors: GE
authors: Crawford
authors: Center for Genomic & Computational Biology, Duke University, Durham, NC 27708, USA; Department of Biostatistics & Bioinformatics, Duke University, Durham, NC 27708, USA. Electronic address: tim.reddy@duke.edu.
authors: Timothy E
authors: TE
authors: Reddy
mesh_terms: D000072283:A549 Cells; D001665:Binding Sites / Q000187:drug effects; D047369:Chromatin Immunoprecipitation; D003907:Dexamethasone / Q000378:metabolism / Q000494:pharmacology; D017930:Genes, Reporter; D015894:Genome, Human; D005938:Glucocorticoids / Q000378:metabolism* / Q000494:pharmacology; D006801:Humans; D011485:Protein Binding / Q000187:drug effects; D011965:Receptors, Glucocorticoid / Q000378:metabolism*; D020218:Response Elements; D014157:Transcription Factors / Q000378:metabolism*; D015533:Transcriptional Activation
chemical_list: D005938:Glucocorticoids; C497713:NR3C1 protein, human; D011965:Receptors, Glucocorticoid; D014157:Transcription Factors; D003907:Dexamethasone