Interplay of BAF and MLL4 promotes enhancer activation

Cell type-specific enhancers are activated by coordinated actions of lineage-determining transcription factors (LDTFs) and chromatin regulators. The SWI/SNF complex BAF and the histone H3K4 methyltransferase MLL4 (KMT2D) are both implicated in enhancer activation. However, the interplay between BAF and MLL4 in enhancer activation remains unclear. Using adipogenesis as a model system, we identify BAF as the major SWI/SNF complex that colocalizes with LDTFs and MLL4 on active enhancers during cell differentiation. Similar to MLL4, BAF is required for cell type-specific gene induction in adipogenesis. In contrast, another SWI/SNF complex PBAF is enriched on promoters and is dispensable for adipogenesis. By depleting BAF subunits SMARCA4 (BRG1) and SMARCB1 (SNF5) as well as MLL4 in cells, we show that BAF and MLL4 reciprocally regulate each other’s binding on active enhancers before and during adipogenesis. By focusing on enhancer activation by the adipogenic transcription factor C/EBPβ without inducing cell differentiation, we provide direct evidence to support an interdependent relationship between BAF and MLL4 in activating cell type-specific enhancers. Together, these findings suggest that the interplay of BAF and MLL4 promotes LDTF-dependent activation of cell type-specific enhancers. Expression profiling by RNA-Seq at D-3, D2 or D7 of adipogenesis in culture, and ChIP-Seq profiling of BAF subunits (Brg1, SS18, Arid1a), PBAF subunit BAF200, GBAF subunit Brd9, MLL4, CBP, histone modifications (H3K4me1 and H3K27ac) by ChIP-seq, profiling of chromatin accessibility by ATAC-Seq at D-3 or D2 of adipogenesis in culture.