GEO series
Foxp3 and BATF cooperatively direct cis-regulatory programs and gene expression for functional differentiation of Treg cells [RNA-seq]
GSE267967
Mus musculus
Expression profiling by high throughput sequencing
26 samples
Submitted 2026/04/29
Platform GPL18480Platform GPL28457
Summary
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.
Published in
Murakami R, Hayatsu N, Miyao T et al.
· Immunity 2026
· PMID 41916318
· doi:10.1016/j.immuni.2026.03.005
This dataset
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Direct links to NCBI, no account and no request form: the whole study as GSE267967_RAW.tar, processed values as the series matrix, the supplementary file directory, and per-sample supplementary files for any of the 26 samples. Raw sequencing reads are also available from ENA.
Also filed as BioProject PRJNA1113962 and SRA study SRP508910. Searching any of these in the dataset finder brings you back here.
Study design
26 conditions, each sampled once — no replicated groups
Read from 26 sample titles: 26 distinct titles with little repetition. Check it against the sample list below before relying on it.
Samples in this study
0 selected
- GSM8282593 WT Treg_1 (RNA-seq)
- GSM8282594 WT Treg_2 (RNA-seq)
- GSM8282595 WT Treg_YFP_1 (RNA-seq)
- GSM8282596 WT Treg_YFP_2 (RNA-seq)
- GSM8282597 BATFKO Treg_1 (RNA-seq)
- GSM8282598 BATFKO Treg_2 (RNA-seq)
- GSM8282599 BATFcKO Treg_YFP_1 (RNA-seq)
- GSM8282600 BATFcKO Treg_YFP_2 (RNA-seq)
- GSM8282601 WT Treg_3 (RNA-seq) (R397W control)
- GSM8282602 WT Treg_4 (RNA-seq) (R397W control)
- GSM8282603 Foxp3R397W Treg_1 (RNA-seq)
- GSM8282604 Foxp3R397W Treg_2 (RNA-seq)
- GSM8282605 WT Treg_5 (RNA-seq) (Foxp3KO control)
- GSM8282606 WT Treg_6 (RNA-seq) (Foxp3KO control)
- GSM8282607 Foxp3KO Treg_1 (RNA-seq)
- GSM8282608 Foxp3KO Treg_2 (RNA-seq)
- GSM8282609 WT cTreg_1 (RNA-seq)
- GSM8282610 WT cTreg_2 (RNA-seq)
- GSM8282611 WT eTreg_1 (RNA-seq)
- GSM8282612 WT eTreg_2 (RNA-seq)
- GSM8282613 WT Tnaive_1 (RNA-seq)
- GSM8282614 WT Tnaive_2 (RNA-seq)
- GSM8282615 WT Teff_1 (RNA-seq)
- GSM8282616 WT Teff_2 (RNA-seq)
- GSM9204526 WT Tconv_1 (RNA-seq)
- GSM9204527 WT Tconv_2 (RNA-seq)
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