Structural and functional properties of mSWI/SNF chromatin remodeling complexes revealed through single-cell perturbation screens

The mammalian SWI/SNF (mSWI/SNF or BAF) family of chromatin remodeling complexes play critical roles in regulating DNA accessibility and gene expression. The three final-form subcomplexes—cBAF, PBAF, and ncBAF—are distinct in biochemical componentry, chromatin targeting, and roles in disease; however, the contributions of their constituent subunits to gene expression remain incompletely defined. Here, we performed Perturb-seq-based CRISPR-Cas9 knockout screens targeting mSWI/SNF subunits individually and in select combinations, followed by single-cell RNA-seq and SHARE-seq. We uncovered complex-, module-, and subunit-specific contributions to distinct regulatory networks and defined paralog subunit relationships and shifted subcomplex functions upon perturbations. Synergistic, intra-complex genetic interactions between subunits reveal functional redundancy and modularity. Importantly, single-cell subunit perturbation signatures mapped across bulk primary human tumor expression profiles both mirror and predict cBAF loss-of-function status in cancer. Our findings highlight the utility of Perturb-seq to dissect disease-relevant gene regulatory impacts of heterogeneous, multi-component master regulatory complexes. [Display omitted] •mSWI/SNF complex-, module-, and subunit-specific impacts defined by Perturb-seq•Perturb- and SHARE-seq define paralog relationships and shifted complex functions•Intra-complex mSWI/SNF genetic interactions are largely synergistic•Single-cell perturbation signatures mirror and predict cBAF loss of function in cancer Otto et al. use Perturb-seq-based single-cell profiling to reveal that chromatin accessibility and gene expression are driven by unique subunits, modules, and subassemblies within the heterogeneous mammalian SWI/SNF family of ATP-dependent chromatin remodeling complexes.