We use several in vitro cell culture models including embryonic stem cells and myeloid cells to understand the role of BAF complexes in transcriptional networks controlling cellular differentiation and response to stimulus.

Biochemical composition and genomic targeting of BAF complexes

We recently discovered a new variant of the BAF complex called the GBAF complex in mouse embryonic stem cells, which contains the bromodomain protein BRD9. Using ChIP-seq against unique subunits in the three BAF complex variants (GBAF, BAF, and PBAF), we discovered that GBAF complexes and canonical BAF complexes are targeted to different sites. While BAF complexes are more commonly found at enhancers, GBAF complexes are found at promoters and topologically-associated domain boundaries, along with CTCF. Importantly, the genomic localization of GBAF complexes is regulated by the binding of the BRD9 bromodomain to acetylated residues. Given that many BAF subunits contain protein domains that interface with chromatin, we are performing biochemical and molecular biology analysis to understand the contribution of these binding domains to complex targeting of BAF complex variants.

Mechanism of action of BAF complexes

We showed that the BAF complex subunit ARID1A regulates chromatin accessibility primarily at enhancers, where it is also essential for maintaining active enhancer architecture in the form of histone modifications and eRNA transcription. We are now examining the role of BAF complex variants in macrophage differentiation and activation to inflammatory stimuli using genetic and chemical perturbation of subunits unique to the GBAF, BAF, and PBAF complexes. Our goal is to build a network defining how these complexes cooperate under basal and stimulated conditions to regulate transcriptional programs.

Role of BAF complexes in Cellular Differentiation

We are using in vitro models of stem cell differentiation to define the role of BAF complexes in cellular differentiation. Using CRISPR engineered cell lines, we have found that mutations in BAF subunits disrupt lineage specification by failing to activate cell type specific enhancers and bivalent promoters. Ultimately, this results in undefined cellular differentiation. This has implications for diseases associated with mutations in BAF subunits, which may arise due to changes in cell identity.