GEO series
Foxp3 and BATF cooperatively direct cis-regulatory programs and gene expression for effector Treg cell differentiation [ChIP-Seq]
GSE267882
Mus musculus
Genome binding/occupancy profiling by high throughput sequencing
34 samples
Submitted 2026/03/31
Platform GPL18480
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 GSE267882_RAW.tar, processed values as the series matrix, the supplementary file directory, and per-sample supplementary files for any of the 34 samples. Raw sequencing reads are also available from ENA.
Also filed as BioProject PRJNA1113592 and SRA study SRP508697. Searching any of these in the dataset finder brings you back here.
Study design
34 conditions, each sampled once — no replicated groups
Read from 34 sample titles: 34 distinct titles with little repetition. Check it against the sample list below before relying on it.
Samples in this study
0 selected
- GSM8281045 WT_Treg_1 (BATF ChIP-seq)
- GSM8281046 WT_Treg_2 (BATF ChIP-seq)
- GSM8281047 WT_Tconv_1 (BATF ChIP-seq)
- GSM8281048 WT_Tconv_2 (BATF ChIP-seq)
- GSM8281049 WT_Treg (BATF ChIP-seq input)
- GSM8281050 WT_Tconv (BATF ChIP-seq input)
- GSM8281051 WT_Treg_1 (Foxp3 ChIP-seq)
- GSM8281052 WT_Treg_2 (Foxp3 ChIP-seq)
- GSM8281053 BATFKO_Treg_1 (Foxp3 ChIP-seq)
- GSM8281054 BATFKO_Treg_2 (Foxp3 ChIP-seq)
- GSM8281055 WT_cTreg_1 (Foxp3 ChIP-seq)
- GSM8281056 WT_cTreg_2 (Foxp3 ChIP-seq)
- GSM8281057 WT_eTreg_1 (Foxp3 ChIP-seq)
- GSM8281058 WT_eTreg_2 (Foxp3 ChIP-seq)
- GSM8281059 WT_Treg (Foxp3 ChIP-seq input)
- GSM8281060 BATFKO_Treg (Foxp3 ChIP-seq input)
- GSM8281061 WT_cTreg_1 (Foxp3 ChIP-seq input)
- GSM8281062 WT_cTreg_2 (Foxp3 ChIP-seq input)
- GSM8281063 WT_eTreg_1 (Foxp3 ChIP-seq input)
- GSM8281064 WT_eTreg_2 (Foxp3 ChIP-seq input)
- GSM9204512 WT_Treg_3 (BATF ChIP-seq) (R397W_Treg_control)
- GSM9204513 WT_Treg_4 (BATF ChIP-seq) (R397W_Treg_control)
- GSM9204514 R397W_Treg_1 (BATF ChIP-seq)
- GSM9204515 R397W_Treg_2 (BATF ChIP-seq)
- GSM9204516 WT_Treg (BATF ChIP-seq input) (R397W_Treg_control)
- GSM9204517 R397W_Treg (BATF ChIP-seq input)
- GSM9204518 WT_Treg_1 (IRF4 ChIP-seq)
- GSM9204519 WT_Treg_2 (IRF4 ChIP-seq)
- GSM9204520 WT_Treg_3 (IRF4 ChIP-seq)
- GSM9204521 WT_Treg_4 (IRF4 ChIP-seq)
- GSM9204522 WT_Tconv_1 (IRF4 ChIP-seq)
- GSM9204523 WT_Tconv_2 (IRF4 ChIP-seq)
- GSM9204524 WT_Tconv_3 (IRF4 ChIP-seq)
- GSM9204525 WT_Tconv_4 (IRF4 ChIP-seq)
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