Mechanisms of enhancer-promoter communication, genome organization and transcription control

ABSTRACT Metazoan genomes achieve complex gene control by uncoupling regulatory DNA elements from target promoters and allowing regulation at a distance. Thus, a gene can be differentially expressed in different cell types and under different environmental signals or developmental cues. How distal regulatory elements (enhancers) target specific gene promoters, how the search process is shaped by the topology of the genome in the nucleus and how enhancer-promoter interactions are facilitated by regulatory complexes that relay signals to the RNA Polymerase II and control transcription activity remains a mystery. Our goal is to understand molecular and biophysical mechanisms that enable enhancer-promoter communication in human and other mammalian cells. Towards these goals and during the period of this award we will accomplish the following: (i) visualize the dynamic communication of enhancers and target promoters simultaneously with the association of regulatory complexes and gene activity, using novel single-molecule and super-resolution approaches for non-invasive 4D imaging of structure and function of the genome in single live cells; (ii) determine mechanisms by which different classes of architectural proteins shape genome folding, enhancer- promoter communication and transcription kinetics; (iii) dissect the function and interdependencies of individual constituent enhancer elements within complex regulatory landscapes controlling cell identity genes. Our results will establish quantitative frameworks for understanding the biochemistry of transcription regulation in the crowded environment of the nucleus and for interpreting gene regulation and genome organization using soft- matter/polymer physics and related biophysical concepts. These conceptual leaps are needed to ultimately understand physical chromatin organization at sub-Mb scales, the scale most relevant for regulatory genome interactions. Our integrated structure-function approach will provide functional validation and critical tests for gene “regulation-at-a-distance” models. The proposed studies will not only provide substantial new knowledge on the mechanisms of promoter-enhancer communication but will also set the stage for further studies of the interplay of genome topology/organization and gene expression regulation.