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Series GSE149693 Query DataSets for GSE149693
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
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.
 
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.
 
Contributor(s) Zong X, Xu B, Cross R, Feng Y
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Submission date May 01, 2020
Last update date May 29, 2024
Contact name Beisi Xu
E-mail(s) beisi.xu@stjude.org
Organization name St Jude Children's Research Hosipital
Department Center for Applied Bioinformatics
Street address 262 Danny Thomas Pl
City Memphis
State/province Tennessee
ZIP/Postal code 38105
Country USA
 
Platforms (1)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (16)
GSM4509061 RNA-1835231_minusIL2a
GSM4509062 RNA-1835232_minusIL2b
GSM4509063 RNA-1835233_plusIL2a
This SubSeries is part of SuperSeries:
GSE149674 Dynamic Foxp3-chromatin interaction controls tunable Treg cell function
Relations
BioProject PRJNA629759
SRA SRP259916

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SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE149693_RAW.tar 2.4 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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