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Series GSE34975 Query DataSets for GSE34975
Status Public on Apr 01, 2013
Title The Kdm5c histone demethylase controls enhancer and promoter function.
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Here, we show that the Kdm5c/Smcx member of the Jarid1 family of H3K4 demethylases is recruited to both enhancer and core promoter elements in ES and neuronal progenitor cells (NPC). Knockdown of Kdm5c deregulates transcription via a local increase in H3K4me3. While at core promoters the function of Kdm5c is to restrict transcription, loss of Kdm5c impairs enhancer function. Remarkably, an impaired enhancer function activates promoter activity from Kdm5c-bound intergenic regions. Our results demonstrate that the Kdm5c demethylase plays a crucial role in the functional identity and discrimination of enhancers and core promoters. We speculate that this is related to recruitment of H3K4me3 binders like the TFIID and NURF complexes6-8. Providing functional identity to genomic regions through balancing enzymes that deposit and remove histone modifications may prove to be a general epigenetic mechanism for the functional indexing of eukaryotic genomes.
Overall design Examination of the KDM5C binding sites in mouse embryonic stem cells and in neuronal progenitor cells. Effect of KDM5C knock down on H3K4me3 and H3K4me1 levels and gene expression.
Contributor(s) Outchkourov NS, Timmers HT
Citation(s) 23545502
Submission date Jan 10, 2012
Last update date May 15, 2019
Contact name Richard van Schaik
Organization name UMCUtrecht
Department Molecular Cancer Research
Street address Universiteitsweg 100
City Utrecht
ZIP/Postal code 3584 CG
Country Netherlands
Platforms (1)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (8)
GSM859661 BirA_ChIP_ES
SRA SRP010203
BioProject PRJNA151105

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Supplementary file Size Download File type/resource
GSE34975_RAW.tar 995.9 Mb (http)(custom) TAR (of WIG)
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Raw data are available in SRA
Processed data provided as supplementary file

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