Connecting cohesin and SETD2 in the regulation of genome structure and function

PROJECT SUMMARY The human genome is subject to multiple layers of organization within the nucleus. At the base layer, DNA is packaged into chromatin by associations with histone proteins whose post-translational modification (PTM) govern access to underlying DNA for DNA-templated processes. At a higher level, chromatin is organized into higher-order structures, in-part through DNA loop extrusion by the cohesin complex. Cohesin-mediated loop extrusion serves to bring distal regions of chromatin, including cis-regulatory elements, into proximity to coordinate gene expression. Appropriate regulation of both of these layers of genome organization has critical implications on genome function, and their dysregulation has been implicated in human disease, including and particularly cancer. However, the extent to which these layers influence each other remains unclear. SETD2 is a histone lysine methyltransferase catalyzing H3K36 trimethylation (H3K36me3) in humans with canonical roles in transcription. Recent work has elucidated novel roles for SETD2 unrelated to its functions in transcription, including a role in maintaining nuclear integrity through cell division in a catalysis-independent manner. Proteomics-based assessment of the SETD2 interactome revealed a surprising enrichment of cohesin complex members with SETD2. Preliminary interrogation of this interaction revealed striking parallels with the associations between SETD2 and the nuclear lamina occurring independently of SETD2-mediated H3K36me3, warranting further investigation of whether SETD2 is functioning non-catalytically to co-regulate cohesin function. Moreover, both cohesin and SETD2 have been implicated in the regulation of transcription and splicing, but whether cohesin-SETD2 function in coordination in these contexts is not yet known. Here, I have formulated three specific aims leveraging a multi-omic, cell-based strategy for (i) pinpointing the molecular determinants and timing of the cohesin-SETD2 interaction, (ii) interrogating SETD2 as a co-regulator of cohesin-mediated DNA looping, and (iii) determining the distinct and overlapping contributions of cohesin and SETD2 to transcription and splicing. To date, no examples of functional coordination between a chromatin-modifying enzyme and cohesin-mediated DNA looping have yet been elucidated, leaving this study well-positioned to glean the first insight into how these layers of genome regulation interface with each other. This key insight could help to understand the pathogenesis of human disease characterized in-part by the dysregulation of either SETD2 or cohesin, which can then be leveraged in identifying strategies for preventing and/or resolving such instances.