Role of Nuclear Receptor Condensates in Ligand Induced Co‐operative Gene Regulation

Abstract

Enhancers are transferable DNA elements that regulate target genes within the confines of Topologically Associated Domains (TADs) through Cohesin‐dependent looping. However, the potential regulatory functions and mechanisms of long‐distance, inter‐TAD enhancer associations remain largely unexplored. We report that 17β‐estradiol (E2) rapidly increases the spatial proximity of a fraction of E2‐responsive enhancers located in widely separated TADs. These enhancers are characterized by the recruitment of mega‐dalton sized multi transcription factor complex and high enhancer RNA (eRNA) induction. Optimal activation of these enhancer targets requires their co‐localization with phase‐separated interchromatin granules (ICGs). Chemical disruption of phase‐separated structures abolishes enhancer complex assembly and, specifically deactivates the most robust signal induced enhancers. Surprisingly, the physical property of the enhancer complex alters with the duration of hormone stimulation. In support of the long distance enhancer cooperativity model, the deletion of the most robust E2 induced enhancers resulted in a quantifiable decrease in the transcriptional activity of homotypic enhancers in the same chromosome. These data reveal previously unappreciated mechanisms for co‐ordinated gene regulation: (i) The biophysical properties of enhancer complex is critical for transcriptional output (ii) Phase separation mediated long‐distance enhancer cooperativity is required for optimal transcriptional activation by acute signaling programs. These findings reveal a new, generalizable model for the acute spatial gene regulation.Support or Funding InformationResearch support for S.J.N include postdoctoral fellowship from American Heart Association (14POST19860025), T32 Fellowship (5T32DK007044), and KO1 career grant (1K01DK121871). D.M. was supported by NIH‐NIDDK Grant 5F32DK112682. MGR is supported by Howard Hughes Medical Institute.Model of E2‐induced changes in the chromatin architecture. E2 stimulation results in ERa dependent recruitment of MegaTrans complex, Condensin complex, and enhancer RNA as phase‐separated ribonucleoprotein condensates. Spatial enhancer association results from “megaloops” formation between the most robust enhancers (E.g. TFF1e1 and NRIP1e3). Maximal cooperative enhancer activation occurs with the co‐localization of the enhancers in the interchromatin granule (ICG).Figure 1