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Series GSE54453 Query DataSets for GSE54453
Status Public on Sep 29, 2014
Title CREBBP (CBP) ChIP-seq in wild type and CBP null MEFs +/- dipyridyl
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Genome-wide distribution of histone H3K18 and H3K27 acetyltransferases, Crebbp (CBP) and Ep300 (p300), is used to map enhancers and promoters, but whether these elements functionally require CBP/p300 remains largely uncertain. We investigated this relationship by comparing genomic CBP recruitment with gene expression in wild type and CBP/p300 double-knockout fibroblasts. ChIP-seq revealed nearby CBP recruitment for 20 percent of constitutively expressed genes, but surprisingly, three-quarters of these were unaffected or slightly activated by CBP/p300 deletion. Computationally defined enhancer-promoter-units (EPUs) having a CBP peak within two kilobases of the enhancer-like element provided better predictive value, with CBP/p300 deletion attenuating expression of 40 percent of such EPU assigned constitutively expressed genes. We next examined signaling-responsive (Hypoxia Inducible Factor) gene expression and CBP recruitment, and found that 97 percent of inducible genes were within 50 kilobases of an inducible CBP peak, and 70 percent of these required CBP/p300 for full inducible expression. Unexpectedly however, most inducible CBP peaks occurred near signal-nonresponsive genes.
Overall design eight samples total; Two wild type and two CBP null primary mouse embryonic fibroblast (MEF) lines, each treated with 100uM 2,2-dipyridyl or ethanol vehicle for 2 hours
Contributor(s) Brindle PK, Kasper LH
Citation(s) 25249627
Submission date Jan 28, 2014
Last update date May 15, 2019
Contact name Suzanne J Baker
Organization name St Jude Children's Research Hospital
Department Developmental Neurobiology
Street address 262 Danny Thomas Place
City Memphis
State/province TN
ZIP/Postal code 38105
Country USA
Platforms (1)
GPL11002 Illumina Genome Analyzer IIx (Mus musculus)
Samples (8)
GSM1315600 WT1_DP
GSM1315601 WT2_DP
GSM1315602 CBP_null1_DP
This SubSeries is part of SuperSeries:
GSE54454 Genome-wide and single-cell analyses reveal target gene context-dependent relationship between Crebbp recruitment and both constitutive and signal-responsive gene expression.
BioProject PRJNA236594
SRA SRP035922

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Supplementary file Size Download File type/resource
GSE54453_RAW.tar 1.6 Gb (http)(custom) TAR (of BW)
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Raw data are available in SRA
Processed data provided as supplementary file

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