{"database":"GEO","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Other":["ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE267nnn/GSE267881/"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"omics_type":["Genomics"],"species":["Mus musculus"],"gds_type":["Genome binding/occupancy profiling by high throughput sequencing"],"full_dataset_link":["https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE267881"],"repository":["GEO"],"entry_type":["GSE"],"additional_accession":[]},"is_claimable":false,"name":"Foxp3 and BATF cooperatively direct cis-regulatory programs and gene expression for effector Treg cell differentiation [ATAC-Seq]","description":"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.","dates":{"publication":"2026/03/31"},"accession":"GSE267881","cross_references":{"GSM":["GSM8281026","GSM8281027","GSM8281028","GSM8281029","GSM9209822","GSM9209821","GSM9209823","GSM9209820","GSM8281033","GSM8281034","GSM8281035","GSM8281036","GSM8281030","GSM8281031","GSM8281032","GSM9209819","GSM9209818","GSM8281037","GSM8281038","GSM9209817","GSM8281039","GSM9209816","GSM8281044","GSM8281023","GSM8281024","GSM8281025","GSM8281040","GSM8281041","GSM8281042","GSM8281043"],"GPL":["17021","28457"],"GSE":["267881"],"taxon":["Mus musculus"]}}