FoxP3 conditions the transcriptional signature and functional facets of regulatory T (Treg) cells. Its mechanism of action, whether as an activator or a repressor, remains unclear. Chromatin analysis shows that FoxP3 binds active enhancer elements, not repressed chromatin, around loci over- and under-expressed in Treg cells. We evaluated the impact of a FoxP3 mutation panel on transcriptional activity and interactions with DNA, transcriptional cofactors and chromatin. Computational integration, confirmed by biochemical interaction and size analyses, showed that FoxP3 exists in distinct multimolecular complexes. It is active and primarily an activator when complexed with the transcriptional co-factors RELA, IKZF2, and KAT5. In contrast, FoxP3 is inactive when complexed to EZH2, YY1 and IKZF3, where super-resolution microscopy shows this complex to partition to a peripheral region of the nucleus. Thus, FoxP3 acts in multimodal fashion to directly activate or repress transcription, in a context- and partner-dependent manner, to govern Treg cell phenotypes.
