Genome-wide Binding Potential and Regulatory Activity of the Glucocorticoid Receptor’s Monomeric and Dimeric Forms

A widely regarded model for glucocorticoid receptor (GR) action postulates that dimeric binding to DNA regulates unfavorable metabolic pathways while monomeric receptor binding promotes repressive gene responses related to its anti-inflammatory effects. This model has been built upon the characterization of the GRdim mutant, reported to be incapable of DNA binding and dimerization. Although quantitative live-cell imaging data shows GRdim as mostly dimeric, genomic studies, on the basis of recovery of enriched half-site response elements, suggest monomeric engagement on DNA. Here, we performed genome-wide studies on GRdim and a constitutively monomeric mutant. Our results show that impairing dimerization affects binding to even open chromatin. Also, GRdim does not exclusively bind half-response elements. Our results do not support a physiological role for monomeric GR and are consistent with a common mode of receptor binding via higher order structures that drives both the activating and repressive actions of glucocorticoids. Genome-wide occupancy profiling of GR and active histone marks by ChIP-seq from mouse mammary adenocarcinoma cell lines (3617) knock-out of endogenous GR (3617-KOGR) and stably integrated with GFP-tagged GR mutants, in biological duplicates, using Illumina NextSeq. GR binding data from the 3617-KOGR cells was used as control for GR (GSE108634; GSM2907216-GSM2907223) and input sample from 3617-KOGR cells were used as controls for the rest (GSE108634; GSM2907274). Chromatin accessibility examined by ATAC-seq from GRdim cell line, in biological duplicates, using Illumina HiSeq4000. Gene expression profiling from GR mutant cell lines by RNA-seq, in biological triplicates, using Illumina HiSeq2500.