Investigating SMARCE1 in Regulating Cohesin Activity, Chromatin Folding, and Gene Expression

PROJECT SUMMARY The cohesin complex mediates the hierarchical organization of the genome into chromatin loops and topologically associating domains (TADs) through a proposed model of loop extrusion. Indeed, cohesin plays an important role in human health, since mutations in cohesin cause a developmental disorder known as Cornelia

de Lange Syndrome (CdLS). However, mechanistically, it remains unclear how cohesin dysfunction contributes to the pathogenesis of CdLS. Interestingly, ~30% of CdLS patients do not harbor mutations in known cohesin components highlighting the gap in our understanding of cohesin regulation. Therefore, we reason that unknown

factors are contributing to cohesin function, and that uncovering these factors may reveal mechanistic links between cohesin dysfunction and disease. To this end, we completed screening genome-wide for genes that can modulate chromatin interactions across TADs. We found that SMARCE1, which is a DNA-binding subunit of

the ATP-dependent human chromatin remodeling complex SWI/SNF, promotes inter-TAD interactions, which cohesin also facilitates. We next determined that SMARCE1 genetically interacts with cohesin, suggesting SMARCE1 regulates cohesin-mediated chromatin looping. Strikingly, mutations in SWI/SNF cause Coffin-Siris

Syndrome (CSS), a developmental disorder that shares overwhelming phenotypic overlap with CdLS. The goal of this proposal is to determine how SMARCE1 regulates cohesin and chromatin looping across the genome, and the extent to which a cohesin dysfunction may underlie a shared signature of gene misexpression in CdLS and CSS through two related, but independent aims.

I will first determine the SWI/SNF dependency of SMARCE1 in promoting cohesin-mediated loop extrusion. Next, I will interrogate the consequences of SWI/SNF and SMARCE1 loss on global cohesin localization and chromatin organization. In parallel, I will intersect the changes in chromatin folding following

SMARCE1 depletion with changes in SWI/SNF and cohesin localization. Taking advantage of publicly available genomic datasets, I will also intersect any detected differential looping or cohesin localization in the context of different chromatin states. Furthermore, the novel role of a CSS-associated gene in chromatin folding suggests

that CdLS and CSS may converge on cohesin dysfunction. In addition to the overlapping clinical presentations of CdLS and CSS, I will define the extent to which CdLS and CSS share signatures of cohesin dysfunction in patient-derived cell lines. I will investigate whether chromatin is misfolded in CSS as in CdLS and how this

chromatin misfolding correlates with comparative transcriptomics between CSS and CdLS. As is the case in CdLS, I will determine if any marker of cohesin dysfunction correlates with CSS disease severity. Completion of this proposal will define the role of SMARCE1 in regulating cohesin-mediated chromatin folding and highlight a

potential shared molecular etiology at the intersection of CdLS and CSS providing the foundational knowledge upon which to further explore common therapeutic interventions in more complex in vivo models.