Discovery and characterization of a non-canonical mSWI/SNF complex

Abstract

Mammalian SWI/SNF (mSWI/SNF) complexes are multi-subunit ATP-dependent chromatin remodelers that regulate genomic architecture, and genes encoding subunits of mSWI/SNF are frequently disrupted in a wide variety of human cancers and developmental disorders. While mSWI/SNF complexes are assembled into two distinct final-form configurations, BAF and PBAF, the modular organization and pathway of assembly of these chromatin regulators remain unknown, presenting a major barrier to structural and functional determination. Additionally, complex-specific targeting on chromatin and roles in disease also remain undefined. In efforts to biochemically elucidate the subunit- and subcomplex- specific functions, this dissertation identified a third evolutionarily conserved complex configuration distinct from canonical BAF (cBAF) and PBAF. Specifically, this non-canonical BAF (ncBAF) configuration lacks evolutionarily conserved subunits, such as SMARCB1, and uniquely incorporates BRD9 and a new set of evolutionarily conserved paralogs, GLTSCR1 and GLTSCR1L. To provide insight into the assembly and organization of these three final-form mSWI/SNF configurations, cBAF, PBAF, and ncBAF, we performed affinity purification of endogenous mSWI/SNF complexes from mammalian and Drosophila cells coupled with cross linking-mass spectrometry (CX-MS). We identified three distinct and evolutionarily conserved modules, characterized their organization and temporal incorporation into each final-form mSWI/SNF complex, and defined the requirement of each subunit for complex formation and stability. To elucidate functional differences, we mapped cBAF, PBAF, and ncBAF complexes genome-wide using ChIP-seq, finding they are differentially distributed throughout the genome; cBAF is preferentially enriched at enhancers, PBAF at promoters, and ncBAF at CTCF sites. We identified ncBAF subunits as synthetic lethalities specific to human synovial sarcoma and malignant rhabdoid tumor, which share in common cBAF complex perturbation. Chemical degradation of the BRD9 subunit of ncBAF rapidly attenuates SS and MRT cell proliferation. Notably, in cBAF-perturbed cancers, ncBAF complexes retain their hallmark localization to CTCF sites and promoters, and maintain gene expression at retained mSWI/SNF sites to support cell proliferation in a manner distinct from fusion oncoprotein-mediated targeting. Taken together, these findings provide new insight into the architecture and function of the mammalian SWI/SNF family of chromatin remodeling complexes, and specifically unmask the unique targeting and function of ncBAF complexes along with potential cancer-specific therapeutic targets.