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Series GSE40684 Query DataSets for GSE40684
Status Public on Sep 28, 2012
Title Foxp3 exploits a preexistent enhancer landscape for regulatory T cell lineage specification [ChIP-Seq]
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Regulatory T (Treg) cells, whose identity and function are defined by the transcription factor Foxp3, are indispensable for immune homeostasis. It is unclear whether Foxp3 exerts its Treg lineage specification function through active modification of the chromatin landscape and establishment of new enhancers or by exploiting a pre-existing enhancer landscape. Analysis of the chromatin accessibility of Foxp3-bound enhancers in Treg and Foxp3-negative T cells showed that Foxp3 was bound overwhelmingly to pre-accessible enhancers occupied by its cofactors in precursor cells or a structurally related predecessor. Furthermore, the bulk of Foxp3-bound Treg cell enhancers lacking in Foxp3- CD4+ cells became accessible upon T cell receptor activation prior to Foxp3 expression with only a small subset associated with several functionally important genes being exclusively Treg cell-specific. Thus, in a late cellular differentiation process Foxp3 defines Treg cell functionality in an “opportunistic” manner by largely exploiting the preformed enhancer network instead of establishing a new enhancer landscape.
Overall design Four transcription factors (Foxp3, Ets1, Elf1, and Cbfb) were immunoprecipated while crosslinked to chromatin. These experiments were then combined with DNase-seq data (being uploaded separately as part of ENCODE project) to find that Foxp3 binds exclusively to open chromatin. Data was also leveraged from Foxo1 ChIP-seq performed in GSE40657 and confirmed by Runx/Cbfb ChIP-seq performed in GSE33653.
Contributor(s) Samstein R, Arvey A, Rudensky A
Citation(s) 23021222
Submission date Sep 07, 2012
Last update date May 15, 2019
Contact name Aaron Arvey
Organization name Memorial Sloan-Kettering Cancer Center
Street address 415 E 68th St ZRC 1441
City New York
State/province NY
ZIP/Postal code 10065
Country USA
Platforms (2)
GPL9250 Illumina Genome Analyzer II (Mus musculus)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (11)
GSM999179 Treg Foxp3 ChIP Rep1 (Tech Rep1)
GSM999180 Treg Foxp3 ChIP Rep1 (Tech Rep2)
GSM999181 Treg Input Rep1
This SubSeries is part of SuperSeries:
GSE40686 Foxp3 exploits a preexistent enhancer landscape for regulatory T cell lineage specification
BioProject PRJNA174613
SRA SRP015626

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Supplementary file Size Download File type/resource
GSE40684_RAW.tar 20.8 Mb (http)(custom) TAR (of TXT)
GSE40684_foxp3_peaks.txt.gz 24.3 Kb (ftp)(http) TXT
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Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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