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Series GSE40463 Query DataSets for GSE40463
Status Public on Nov 24, 2012
Title STATs Shape the Active Enhancer Landscape of T Cell Populations
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary Signaling pathways are intimately involved in cellular differentiation, allowing cells to respond to their environment by regulating gene expression. While enhancers are recognized as key elements that regulate selective gene expression, the interplay between signaling pathways and actively used enhancer elements is not clear. Here, we use CD4+ T cells as a model of differentiation, mapping the acquisition of cell-type-specific enhancer elements in T-helper 1 (Th1) and Th2 cells. Our data establish that STAT proteins have a major impact on the acquisition of lineage-specific enhancers and the suppression of enhancers associated with alternative cell fates. Transcriptome analysis further supports a functional role for enhancers regulated by STATs. Importantly, expression of lineage-defining master regulators in STAT-deficient cells fails to fully recover the chromatin signature of STAT-dependent enhancers. Thus, these findings point to a critical role of STATs as environmental sensors in dynamically molding the specialized enhancer architecture of differentiating cells.
Overall design Active enhancer elements were defined as p300-high/H3K4me1-high. Using ChIP-seq, we mapped active enhancer landscapes of two CD4+ T helper cells, Th1 and Th2. To investigate the effect of STAT proteins on this landscape, we profiled active enhancers in the absence of STATs. Overall, STATs deficiency had a major impact on recruitment of p300. In addition, ectopic expression of master regulators T-bet and GATA3 in STAT-deficient cells failed to recover most active enhancers.
Contributor(s) Vahedi G, Takahashi H, Nakayamada S, Sun H, Sartorelli V, Kanno Y, O’Shea JJ
Citation(s) 23178119, 23555662
Submission date Aug 29, 2012
Last update date Feb 12, 2020
Contact name Golnaz Vahedi
Organization name National Institutes of Health
Department NIAMS
Lab Lymphocyte Cell Biology Section
Street address 9000 Rockville Pike Bldg 10 Rm 13C101A
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
Platforms (2)
GPL9250 Illumina Genome Analyzer II (Mus musculus)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (42)
GSM994508 p300WTTh1
GSM994509 p300S4KO
GSM994510 p300TbetKO
BioProject PRJNA174565
SRA SRP015458

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Supplementary file Size Download File type/resource
GSE40463_RAW.tar 1.9 Gb (http)(custom) TAR (of BEDGRAPH, BIGWIG, RPKM)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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