Canonical BAF chromatin remodeling complex specifies stem cell fate via cell-type-specific co-factor recruitment.

Individual subunits within the canonical BAF (cBAF) chromatin remodeling complex are known to regulate stem cell behavior, with some functional redundancy across subunits. Yet, how the cBAF complex directs adult stem cell fate specification and maintains stem cell niches remains unclear. Using the adult mouse incisor, we show that cBAF specifies mesenchymal stem cell (MSC) fate by recruiting distinct transcriptional co-factors to shape cell-type-specific chromatin regulation. Through single-cell multi-omics and in vivo functional analyses, we identify ARID1-containing cBAF as an essential gatekeeper that maintains the dynamic balance between MSC self-renewal and differentiation. Specifically, cBAF-DLX2 interactions preserve niche identity by remodeling intronic chromatin accessibility of niche-defining marker Runx2, while cBAF-FOXO1 directly modulates promoter accessibility of lineage-regulating transcription factors, including STAT3 and TRP53, among others, to balance progenitor proliferation and differentiation. Functional perturbation of RUNX2 and TRP53 confirms their roles downstream of cBAF in niche maintenance and fate specification. Our findings establish cBAF as a central regulator of adult stem cell niches and lineage commitment, and highlight cofactor-dependent mechanisms that may have broader implications for tissue regeneration and BAF-associated disorders.