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 pa-ralog subunit relationships and shifted subcomplex functions upon perturbations. Synergistic, intra-com-plex genetic interactions between subunits reveal functional redundancy and modularity. Importantly, sin-gle-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 Per-turb-seq to dissect disease-relevant gene regulatory impacts of heterogeneous, multi-component master regulatory complexes.

Automated summary

The mammalian SWI/SNF (mSWI/SNF or BAF) family of chromatin remodeling complexes are important for regulating DNA accessibility and gene expression. In this study, Perturb-seq-based CRISPR-Cas9 knockout screens were performed to investigate the roles of individual subunits of mSWI/SNF. The findings reveal the specific contributions of subunits to gene regulatory networks and highlight the potential of Perturb-seq in dissecting the impacts of multi-component master regulatory complexes.