A Genome-wide CRISPR Screen Reveals a Role for the Non-canonical Nucleosome-Remodeling BAF Complex in Foxp3 expression and regulatory T cell function

Regulatory T cells (Treg) play a pivotal role in suppressing auto-reactive T cells and maintaining immune homeostasis. Treg development and function are dependent on the transcription factor Foxp3. Although a large body of work has been devoted to dissecting the molecular mechanisms regulating Foxp3 expression, a systematic, genome-wide approach has not been elucidated. In this study, we performed genome-wide CRISPR loss-of-function screens to identify Foxp3 regulators in mouse primary Treg cells. The screen results not only confirmed a number of known Foxp3 regulators but also revealed many novel factors that control Foxp3 expression. Gene ontology analysis showed Foxp3 regulators were highly enriched in genes encoding subunits of the SWI/SNF nucleosome remodeling and SAGA chromatin modifying complexes. Among the three SWI/SNF-related complexes, the Brd9-containing non-canonical (nc)BAF complex promoted Foxp3 expression, whereas the PBAF complex was repressive. Gene ablation or chemical-induced degradation of Brd9 led to reduced Foxp3 expression and reduced Treg function. Brd9 ablation compromised Treg function in inflammatory disease and tumor immunity. Furthermore, Brd9 promoted Foxp3 binding and expression of a subset of Foxp3 target genes, indicating that Brd9 actively participates in the Foxp3-dependent transcriptional program. In summary, this work provides an unbiased analysis of the genetic networks regulating Foxp3 and reveal ncBAF as a target for therapeutic manipulation of Treg function.