title: Comparison of endogenous and overexpressed MyoD shows enhanced binding of physiologically bound sites.
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.
authors.affiliation: Human Biology Division, Seattle, WA, USA.
authors.forename: Zizhen
authors.initials: Z
authors.lastname: Yao
authors.affiliation: Clinical Research Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA, 98109, USA.|Department of Pediatrics, University of Washington, School of Medicine, Seattle, WA, 98105, USA.
authors.forename: Abraham P
authors.initials: AP
authors.lastname: Fong
authors.affiliation: Bioinformatics and Computational Biology, Genentech, South San Francisco, CA, USA.
authors.forename: Yi
authors.initials: Y
authors.lastname: Cao
authors.affiliation: Departments of Computer Science and Engineering and Genome Sciences, Seattle, WA, USA.
authors.forename: Walter L
authors.initials: WL
authors.lastname: Ruzzo
authors.affiliation: Bioinformatics and Computational Biology, Genentech, South San Francisco, CA, USA.
authors.forename: Robert C
authors.initials: RC
authors.lastname: Gentleman
authors.affiliation: Human Biology Division, Seattle, WA, USA.|Clinical Research Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA, 98109, USA.|Department of Neurology, University of Washington, School of Medicine, Seattle, WA, 98105, USA.
authors.forename: Stephen J
authors.initials: SJ
authors.lastname: Tapscott