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Series GSE80520 Query DataSets for GSE80520
Status Public on Apr 22, 2016
Title The genomic context and co-recruitment of SP1 affect ERRα co-activation by PGC-1α in muscle cells [ChIP-Seq]
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary The peroxisome proliferator-activated receptor γ co-activator 1α (PGC-1α) coordinates the transcriptional network response to promote an improved endurance capacity in skeletal muscle, e.g. by co-activating the estrogen-related receptor α (ERRα) in the regulation of oxidative substrate metabolism. Despite a close functional relationship, the interaction between these two proteins has not been studied on a genomic level. We now mapped the genome-wide binding of ERRα to DNA in skeletal muscle cell line with elevated PGC-1α and linked the DNA recruitment to global PGC-1α target gene regulation. We found that, surprisingly, ERRα co-activation by PGC-1α is only observed in the minority of all PGC-1α recruitment sites. Nevertheless, a majority of PGC-1α target gene expression is dependent on ERRα. Intriguingly, the interaction between these two proteins is controlled by the genomic context of response elements, in particular the relative GC and CpG content, monomeric and dimeric repeat binding site configuration for ERRα, and adjacent recruitment of the transcription factor SP1. These findings thus not only reveal an unprecedented insight into the regulatory network underlying muscle cell plasticity, but also strongly link the genomic context of DNA response elements to control transcription factor - co-regulator interactions.
 
Overall design We performed ChIP-Seq experiments to identify all DNA recruitment sites for ERRalpha in C2C12 cells, in presence of PGC-1alpha over-expression, on a genome-wide scale. The Whole Cell Extract (WCE; =input DNA) was used as background condition.
 
Contributor(s) Salatino S, Kupr B, Baresic M, van Nimwegen E, Handschin C
Citation(s) 27182621
Submission date Apr 21, 2016
Last update date May 15, 2019
Contact name Christoph Handschin
Organization name Biozentrum, University of Basel
Street address Spitalstrasse 41
City Basel
ZIP/Postal code 4056
Country Switzerland
 
Platforms (1)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (2)
GSM2129643 IP_ERRa
GSM2129644 WCE
This SubSeries is part of SuperSeries:
GSE80522 The genomic context and co-recruitment of SP1 affect ERRα co-activation by PGC-1α in muscle cells
Relations
BioProject PRJNA319184
SRA SRP073656

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Supplementary file Size Download File type/resource
GSE80520_ERRa_peaks.bed.gz 22.3 Kb (ftp)(http) BED
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Raw data are available in SRA
Processed data are available on Series record

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