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| Status |
Public on Jun 16, 2014 |
| Title |
Transcriptional network analysis in muscle reveals AP-1 as a partner of PGC-1α in the regulation of the hypoxic gene program [ChIP-Seq] |
| Organism |
Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
Skeletal muscle tissue shows an extraordinary cellular plasticity, but the underlying molecular mechanisms are still poorly understood. Here we use a combination of experimental and computational approaches to unravel the complex transcriptional network of muscle cell plasticity centered on the peroxisome proliferator-activated receptor γ coactivator 1α (PGC-1α), a regulatory nexus in endurance training adaptation. By integrating data on genome-wide binding of PGC-1α and gene expression upon PGC-1α over-expression with comprehensive computational prediction of transcription factor binding sites (TFBSs), we uncover a hitherto underestimated number of transcription factor partners involved in mediating PGC-1α action. In particular, principal component analysis of TFBSs at PGC-1α binding regions predicts that, besides the well-known role of the estrogen-related receptor α (ERRα), the activator protein-1 complex (AP-1) plays a major role in regulating the PGC-1α-controlled gene program of hypoxia response. Our findings thus reveal the complex transcriptional network of muscle cell plasticity controlled by PGC-1α.
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| Overall design |
We performed ChIP-Seq experiments to identify all DNA recruitment sites for PGC-1alpha in C2C12 cells on genome-wide scale. The experiment was performed in duplicate and the Whole Cell Extract (WCE; =input DNA) was used as background condition.
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| Contributor(s) |
Baresic M, Salatino S, van Nimwegen E, Handschin C, Kupr B |
| Citation(s) |
24912679 |
| Submission date |
Sep 25, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Christoph Handschin |
| Organization name |
Biozentrum, University of Basel
|
| Street address |
Spitalstrasse 41
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| City |
Basel |
| ZIP/Postal code |
4056 |
| Country |
Switzerland |
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| Platforms (2) |
| GPL9250 |
Illumina Genome Analyzer II (Mus musculus) |
| GPL11002 |
Illumina Genome Analyzer IIx (Mus musculus) |
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| Samples (4)
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| This SubSeries is part of SuperSeries: |
| GSE51191 |
Transcriptional network analysis in muscle reveals AP-1 as a partner of PGC-1α in the regulation of the hypoxic gene program |
|
| Relations |
| BioProject |
PRJNA221528 |
| SRA |
SRP030459 |
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