A genome-wide CRISPR screen reveals a role for the BRD9-containing non-canonical BAF complex in Foxp3 expression and regulatory T cell function

Abstract

Abstract Regulatory T cells (Tregs) 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 reported. Here we performed a genome-wide CRISPR/Cas9 knockout screen to identify the regulators of Foxp3 in mouse primary natural Tregs. 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 that Foxp3 regulators are highly enriched in genes encoding SWI/SNF and SAGA complex subunits. Among the three SWI/SNF-related complexes, the non-canonical or ncBAF (also called GBAF or BRD9-containing BAF) complex promoted the expression of Foxp3, whereas the PBAF complex repressed its expression. Gene ablation of BRD9 led to reduced Foxp3 expression and compromised Treg function in inflammatory disease and anti-tumor immunity. BRD9 co-localized with Foxp3 in genome-wide binding studies, including at the CNS0 and CNS2 enhancers at the Foxp3 locus. Functional genomics revealed that BRD9 is required for Foxp3 binding and expression of a subset of Foxp3 target genes. Thus, we provide an unbiased analysis of genes and networks regulating Foxp3, and reveal the ncBAF complex as a novel target that could be exploited to manipulate Treg function.