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Yao Z, Fong AP, Cao Y, et al. Comparison of endogenous and overexpressed MyoD shows enhanced binding of physiologically bound sites. Skelet Muscle. 2013;3(1):8doi: 10.1186/2044-5040-3-8.
Yao, Z., Fong, A. P., Cao, Y., Ruzzo, W. L., Gentleman, R. C., & Tapscott, S. J. (2013). Comparison of endogenous and overexpressed MyoD shows enhanced binding of physiologically bound sites. Skeletal muscle, 3(1), 8. https://doi.org/10.1186/2044-5040-3-8
Yao, Zizhen, et al. "Comparison of endogenous and overexpressed MyoD shows enhanced binding of physiologically bound sites." Skeletal muscle vol. 3,1 (2013): 8. doi: https://doi.org/10.1186/2044-5040-3-8
Yao Z, Fong AP, Cao Y, Ruzzo WL, Gentleman RC, Tapscott SJ. Comparison of endogenous and overexpressed MyoD shows enhanced binding of physiologically bound sites. Skelet Muscle. 2013 Apr 08;3(1):8. doi: 10.1186/2044-5040-3-8. PMID: 23566431; PMCID: PMC3666993.
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Skelet Muscle. 2013 Apr 08;3(1):8. doi: 10.1186/2044-5040-3-8.

Comparison of endogenous and overexpressed MyoD shows enhanced binding of physiologically bound sites.

Skeletal muscle

Zizhen Yao, Abraham P Fong, Yi Cao, Walter L Ruzzo, Robert C Gentleman, Stephen J Tapscott

Affiliations

  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. Department of Pediatrics, University of Washington, School of Medicine, Seattle, WA, 98105, USA.
  4. Bioinformatics and Computational Biology, Genentech, South San Francisco, CA, 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.

PMID: 23566431 PMCID: PMC3666993 DOI: 10.1186/2044-5040-3-8

Abstract

BACKGROUND: 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.

METHODS: 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.

RESULTS: 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.

CONCLUSIONS: 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.

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