GEO series
Foxp3 and BATF cooperatively direct cis-regulatory programs and gene expression for effector Treg cell differentiation [scMultiome]
GSE267884
Mus musculus
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
16 samples
Submitted 2026/03/31
Platform GPL24247
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 GSE267884_RAW.tar, processed values as the series matrix, the supplementary file directory, and per-sample supplementary files for any of the 16 samples. Raw sequencing reads are also available from ENA.
Also filed as BioProject PRJNA1113590 and SRA study SRP508704. Searching any of these in the dataset finder brings you back here.
Study design
16 conditions, each sampled once — no replicated groups
Read from 16 sample titles: 16 distinct titles with little repetition. Check it against the sample list below before relying on it.
Samples in this study
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- GSM8281073 WT_Treg_1 (scMultiome, GEX)
- GSM8281074 WT_Treg_2 (scMultiome, GEX)
- GSM8281075 WT_Tconv_1 (scMultiome, GEX)
- GSM8281076 WT_Tconv_2 (scMultiome, GEX)
- GSM8281077 BATFKO_Treg_1 (scMultiome, GEX)
- GSM8281078 BATFKO_Treg_2 (scMultiome, GEX)
- GSM8281079 Foxp3R397W_Treg_1 (scMultiome, GEX)
- GSM8281080 Foxp3R397W_Treg_2 (scMultiome, GEX)
- GSM8281081 WT_Treg_1 (scMultiome, ATAC)
- GSM8281082 WT_Treg_2 (scMultiome, ATAC)
- GSM8281083 WT_Tconv_1 (scMultiome, ATAC)
- GSM8281084 WT_Tconv_2 (scMultiome, ATAC)
- GSM8281085 BATFKO_Treg_1 (scMultiome, ATAC)
- GSM8281086 BATFKO_Treg_2 (scMultiome, ATAC)
- GSM8281087 Foxp3R397W_Treg_1 (scMultiome, ATAC)
- GSM8281088 Foxp3R397W_Treg_2 (scMultiome, ATAC)
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