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GEO help: Mouse over screen elements for information. |
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| Status |
Public on May 28, 2024 |
| Title |
Dynamic Foxp3-chromatin interaction controls tunable Treg cell function [RNA-seq] |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Nuclear factor Foxp3 determines regulatory T (Treg) cell fate and function via mechanisms that remain unclear. Here we investigate the nature of Foxp3-mediated gene regulation in suppressing autoimmunity and antitumor immune response. Contrasting with previous models, we find that Foxp3-chromatin binding is regulated by Treg activation states, tumor microenvironment, and antigen and cytokine stimulations. Proteomics studies uncovered dynamic proteins within the Foxp3 proximity upon TCR or IL-2 receptor signaling in vitro, reflecting intricate interactions among Foxp3, signal transducers, and chromatin. Pharmacological inhibition and genetic knockdown experiments indicate that NFAT and AP-1 protein Batf are required for enhanced Foxp3-chromatin binding in activated Treg cells and tumor-infiltrating Treg cells to modulate target gene expression. Furthermore, mutations at Foxp3 DNA-binding domain destabilize Foxp3-chromatin association. These representative settings delineate context-dependent Foxp3-chromatin interaction, suggesting that Foxp3 associates with chromatin by hijacking DNA-binding proteins resulting from Treg activation or differentiation, which is stabilized by direct Foxp3-DNA binding, to dynamically regulate Treg cell function according to immunological contexts.
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| Overall design |
We developed a comparative proteomics method by projecting the spatial information (PSI) of nuclear proteins with peroxidase–mediated proximity ligation, thus revealing the protein components of the cis-regulatory elements bound by Treg lineage–specifying factor Foxp3. We performed RNA sequencing for naïve CD4 T cells (Tn, CD4+ GFP- CD25- CD44low CD62Lhigh), effector CD4 T cells (aTe, CD4+ GFP- CD44high CD62Llow), resting Treg cells (rTreg, CD4+ GFP+ CD44low CD62Lhigh), and activated Treg cells (aTreg, CD4+ GFP+ CD44high CD62Llow) sorted from 8-10 week old male Foxp3-gfp knockin mice. To reveal signal-dependent transcriptional regulation, we first induced Treg cells in vitro (iTreg) from CD4 naïve T cells isolated from male Foxp3-gfp mice with TCR agonists, Interleukion-2 (IL-2), TGF-beta, and ascorbic acid and then stimulated them with IL-2 for 30 min or with plate-bound anti-CD3 and anti-CD28 antibodies for 3 hours. After stimulation, cells were immediately lysed with the TRIzol reagent for RNA extraction and sequencing.
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| Contributor(s) |
Zong X, Xu B, Cross R, Feng Y |
| Citation(s) |
38935023 |
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| Submission date |
May 01, 2020 |
| Last update date |
Aug 27, 2024 |
| Contact name |
Beisi Xu |
| E-mail(s) |
beisi.xu@stjude.org
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| Organization name |
St Jude Children's Research Hosipital
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| Department |
Center for Applied Bioinformatics
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| Street address |
262 Danny Thomas Pl
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| City |
Memphis |
| State/province |
Tennessee |
| ZIP/Postal code |
38105 |
| Country |
USA |
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| Platforms (1) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
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| Samples (16)
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| This SubSeries is part of SuperSeries: |
| GSE149674 |
Dynamic Foxp3-chromatin interaction controls tunable Treg cell function |
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| Relations |
| BioProject |
PRJNA629759 |
| SRA |
SRP259916 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE149693_RAW.tar |
2.4 Mb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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