E-GEOD-40685 - Transcription profiling by array of mouse Foxp3 knockout regulatory T cells

Status
Released on 28 September 2012, last updated on 28 March 2013
Organism
Mus musculus
Samples (11)
Array (1)
Protocols (7)
Description
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 inaccessible 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. Array expression. Three cell types with 3-5 replicates each.
Experiment type
transcription profiling by array 
Contacts
Aaron Arvey <aarvey@cbio.mskcc.org>, Alexander Rudensky, Robert M Samstein
Citation
Foxp3 exploits a pre-existent enhancer landscape for regulatory T cell lineage specification. Samstein RM, Arvey A, Josefowicz SZ, Peng X, Reynolds A, Sandstrom R, Neph S, Sabo P, Kim JM, Liao W, Li MO, Leslie C, Stamatoyannopoulos JA, Rudensky AY. , Europe PMC 23021222
MIAME
PlatformsProtocolsFactorsProcessedRaw
Files
Investigation descriptionE-GEOD-40685.idf.txt
Sample and data relationshipE-GEOD-40685.sdrf.txt
Raw data (1)E-GEOD-40685.raw.1.zip
Processed data (1)E-GEOD-40685.processed.1.zip
Array designA-AFFY-45.adf.txt
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