Interrogating the Compositional and Functional Diversity of mSWI/SNF Complexes

Abstract

The mammalian SWI/SNF (mSWI/SNF or BAF) family of chromatin remodeling complexes plays an integral role in the regulation of transcription. Nearly 30 mSWI/SNF subunits have been identified and assemble to form subcomplexes that appear to have distinct cellular roles. In this thesis, we begin by interrogating whether all mSWI/SNF subunits had been identified. Through a combination of proteomic, biochemical, and genomic assays, we identify two novel mSWI/SNF subunits, GLTSCR1 and GLTSCR1L. Moreover, we discover that these proteins are mutually exclusive subunits of a novel non-canonical mSWI/SNF (ncBAF) complex that is also uniquely marked by BRD9. Furthermore, we find that the ncBAF complex is a susceptibility in synovial sarcomas and malignant rhabdoid tumors, cancers which both possess disease-driving perturbations of mSWI/SNF complexes. In order to characterize the function of the ncBAF complex, we study the localization of the complex on chromatin using ChIP-seq. Notably, while the known canonical BAF (cBAF) and polybromo-associated BAF (PBAF) complexes associate with enhancers and promoters, respectively, ncBAF complexes associate with the binding sites of CTCF, a protein involved in the establishment and maintenance of chromatin architecture. Next, we note that ncBAF complexes preferentially occupy promoter-proximal CTCF sites, specifically those that engage in DNA looping to enhancers, which have been recently identified as CTCF-mediated enhancer docking sites. Surprisingly, we find that genomic and chemical perturbations of the ncBAF complex do not alter chromatin accessibility, in contrast to experimental observations made in studying other mSWI/SNF complexes such as the canonical BAF complex. Instead, our results suggest that ncBAF plays a role in limiting the occupancy of DNA looping factors, CTCF and SMC1, to CTCF sites. And, while subunits specific to ncBAF are mutated less frequently than those of cBAF and PBAF, we find that putative ncBAF-bound CTCF sites on the genome are enriched for somatic mutations that can result in dysregulation of proximal gene expression. Taken together, these results suggest that the newly-identified ncBAF complex regulates chromatin architecture and transcription through an unexpected mechanism.