GEOapplication/xmlftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE267nnn/GSE267967/primaryOK200TranscriptomicsMus musculusExpression profiling by high throughput sequencinghttps://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE267967GEOGSEfalseFoxp3 and BATF cooperatively direct cis-regulatory programs and gene expression for functional differentiation of Treg cells [RNA-seq]Mechanisms by which diverse transcription factors (TFs), particularly the master regulator Foxp3, shape the heterogeneous transcriptional and epigenetic landscape of regulatory T (Treg) cells remain poorly understood. Here, we discovered that Foxp3 cooperates with BATF to direct cis-regulatory programs and gene expression essential for 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 cell-specific BATF and eTreg cell-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 interacts with specific TFs to orchestrate diverse cis-regulatory programs among Treg cell 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 landscape critical for functional Treg cell differentiation.2026/04/29GSE267967GSM8282614GSM8282615GSM8282616GSM8282610GSM8282599GSM8282611GSM8282612GSM8282613GSM8282603GSM9204526GSM8282604GSM8282605GSM8282606GSM8282600GSM8282601GSM8282602GSM9204527GSM8282607GSM8282608GSM8282609GSM8282595GSM8282596GSM8282597GSM8282598GSM8282593GSM82825941848028457267967Mus musculus