Comparison of endogenous and overexpressed MyoD shows enhanced binding of physiologically bound sites
- Equal contributors
1 Human Biology Division, Seattle, WA, USA
2 Clinical Research Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA, 98109, USA
3 Bioinformatics and Computational Biology, Genentech, South San Francisco, CA, USA
4 Department of Pediatrics, University of Washington, School of Medicine, Seattle, WA, 98105, USA
5 Departments of Computer Science and Engineering and Genome Sciences, Seattle, WA, USA
6 Department of Neurology, University of Washington, School of Medicine, Seattle, WA, 98105, USA
Skeletal Muscle 2013, 3:8 doi:10.1186/2044-5040-3-8Published: 8 April 2013
Transcription factor overexpression is common in biological experiments and transcription factor amplification is associated with many cancers, yet few studies have directly compared the DNA-binding profiles of endogenous versus overexpressed transcription factors.
We analyzed MyoD ChIP-seq data from C2C12 mouse myotubes, primary mouse myotubes, and mouse fibroblasts differentiated into muscle cells by overexpression of MyoD and compared the genome-wide binding profiles and binding site characteristics of endogenous and overexpressed MyoD.
Overexpressed MyoD bound to the same sites occupied by endogenous MyoD and possessed the same E-box sequence preference and co-factor site enrichments, and did not bind to new sites with distinct characteristics.
Our data demonstrate a robust fidelity of transcription factor binding sites over a range of expression levels and that increased amounts of transcription factor increase the binding at physiologically bound sites.