Genomic determination of the glucocorticoid response reveals unexpected mechanisms of gene regulation

Cortisol is a glucocorticoid steroid hormone released by the adrenal glands in response to acute stress and as a messenger in circadian rhythms. Transcriptional responses to this hormonal signal are mediated by the glucocorticoid receptor (GR). Here, using massively parallel DNA sequencing, we determine GR binding across the human genome (using ChIP-seq) and measure related changes in gene expression (using mRNA-seq) in response to the glucocorticoid dexamethasone (DEX). We identify 4,392 genomic positions occupied by the GR and 234 genes with significant changes in expression in response to DEX. This genomic census reveals striking differences between activating and repressing activity of the GR. First, genes activated by DEX have GR occupancy within a median distance of 10 kb from the transcriptional start site (TSS) while, for the genes repressed by DEX, the nearest GR binding site is a median of 150 kb from the TSS. Furthermore, a reduction of GR levels by siRNA significantly and substantially reduces activation of GR target genes, but repression of transcription by DEX was largely unaffected. These results suggest that DEX-mediated repression occurs independently of promoter proximal GR binding and is less sensitive to a reduction in the level of GR. We also find that the GR can distinguish between different levels of corticosteroids in a gene-specific manner by, for example, selectively inducing PER1, a major transcription factor in circadian rhythms, at low doses of DEX. Overall, our work both provides a genome-wide analysis of GR:DNA binding and transcriptional response and also reveals substantial new insights into the gene regulatory activities managed by GR.