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.
Competing Interests: Declaration of interests C.K. is the Scientific Founder, Scientific Advisor to the Board of Directors, Scientific Advisory Board member, shareholder, and consultant for Foghorn Therapeutics, Inc. (Cambridge, MA); serves on the Scientific Advisory Boards of Nereid Therapeutics, Nested Therapeutics, and Fibrogen, Inc.; and is a consultant for Cell Signaling Technologies and Google Ventures. C.K. is also a member of the Molecular Cell advisory board. A.R. is a founder and equity holder of Celsius Therapeutics, an equity holder in Immunitas Therapeutics, and until July 31, 2020 was an SAB member of Syros Pharmaceuticals, Neogene Therapeutics, Asimov and ThermoFisher Scientific. Since August 1, 2020, A.R. has been an employee of Genentech and has equity in Roche. Since May 24, 2021, O.U. has been an employee of Genentech and has equity in Roche. J.E.O. is an employee and equity holder of Flagship Labs 84, Inc.
(Copyright © 2023 The Author(s). Published by Elsevier Inc. All rights reserved.)