Deciphering the Stepwise Regulatory Mechanisms of Genome Folding

Deciphering the Stepwise Regulatory Mechanisms of Genome Folding In multicellular organisms, the precise regulation of gene expression across the different cell types and developmental stages is achieved through the orchestration of cis-regulatory elements, notably enhancers. These elements are positioned distantly from gene promoters and exert their function by establishing physical interactions with them. Crucially, these interactions depend on the three-dimensional folding of the genome. Any disruptions to this highly orchestrated genome folding, which can give rise to dysregulated gene expression, have been implicated in the pathogenesis of a myriad of diseases, including cancer and developmental disorders. Hence, unraveling the mechanisms that govern genome folding becomes a paramount endeavor in order to gain a comprehensive understanding of the precise control of gene expression, both in healthy physiological contexts and in the aberrant states associated with disease. Over the last two decades, significant advancements in genomic studies employing proximity-ligation and sequencing techniques have revealed the cohesin complex as a key driver of genome folding. Recent groundbreaking single-molecule imaging experiments have demonstrated cohesin's motor activity, directly engaging in loop extrusion to fold linear DNA in vitro. However, it has been largely elusive how cohesin-mediated genome folding is regulated in the living cells. To answer this question, we will focus on three research topics: 1. How do nuclear bodies influence cohesin function? 2. What are the post-translational modifications (PTMs) on cohesin-associated factors and their impact on genome folding? 3. What are the cytosolic signals that regulate genome folding through cohesin and how do they do so? Cohesin-mediated genome folding is achieved through highly dynamic processes of cohesin loading/loop extrusion, extrusion stalling, and cohesin unloading. We will dissect and pinpoint the specific process within the genome folding that are regulated by nuclear bodies, PTMs and cytosolic signals. Collectively, our proposed studies aim to unveil novel molecular mechanisms governing genome folding, providing a comprehensive understanding of how genome folding is regulated in living cells and its contribution to disease states.