Ep300 sequestration to functionally distinct glucocorticoid receptor binding loci underlie rapid gene activation and repression

The transcription factor glucocorticoid receptor (GR) is a key mediator of stress response and a broad range of physiological processes. How can GR rapidly activate the expression of some genes while repress others, remains an open question due to the challenge to associate GR binding sites (GBSs) to their distant gene targets. Mapping the 3D scope of GR-responsive promoters using high-resolution 4C-seq unravelled spatial separation between chromatin interaction networks of GR-activated and repressed genes. The spatial compartments of GR-activated and GR-repressed genes vary in the types and configuration of their residing regulatory elements. GR binding to chromatin sequester the co-activator Ep300 from non-GR regulatory loci in GR-activated and repressed gene compartments. While this allows rapid gene repression, effective Ep300 recruitment to GR binding sites positioned within the activated compartments provide the basis for gene induction. Moreover, focused analysis on GBS together with other regulatory loci that cluster in the GR activated compartments identifies ROR, Rev-erb, and Klf4 transcription factors as co-regulators for GR-mediated gene expression. Thus spatial crosstalk between various regulatory loci in GR-responsive compartments provides the basis for precise transcriptional response RNA seq of GFP/EP300 over expression before and after 1h of DEX treatment