Foxp3 and BATF cooperatively direct cis-regulatory programs and gene expression for effector Treg cell...

Mechanisms by which diverse transcription factors (TFs), particularly the master regulator Foxp3, shape the heterogeneous transcriptional and epigenetic landscapes of regulatory T (Treg) cells remain poorly understood. Here, we show that Foxp3 cooperates with BATF to direct cis-regulatory programs and gene expression essential for the differentiation of immunosuppressive effector Treg (eTreg) cells. Simultaneous single-cell chromatin accessibility and transcriptome profiling, combined with topic modeling, identified cis-regulatory elements and associated programs jointly regulated by these TFs in eTreg cells. Genome-wide mapping of Treg-specific BATF and eTreg-specific Foxp3 binding sites revealed their co-binding at some of these cis-elements, synergistically enhancing accessibility and transcription. Furthermore, we provide evidence that Foxp3 cooperates with or counteracts specific TFs to orchestrate diverse cis-regulatory programs across Treg differentiation states. Thus, Foxp3 serves as a master but context-dependent regulator, cooperating with other TFs, including BATF, to shape the heterogeneous cis-regulatory and transcriptional landscapes critical for functional Treg cell differentiation.