Proteome-wide profiling of activated transcription factors with a concatenated tandem array of transcription factor response elements

Proc Natl Acad Sci U S A. 2013 Apr 23;110(17):6771-6. doi: 10.1073/pnas.1217657110. Epub 2013 Apr 3.


Transcription factors (TFs) are families of proteins that bind to specific DNA sequences, or TF response elements (TFREs), and function as regulators of many cellular processes. Because of the low abundance of TFs, direct quantitative measurement of TFs on a proteome scale remains a challenge. In this study, we report the development of an affinity reagent that permits identification of endogenous TFs at the proteome scale. The affinity reagent is composed of a synthetic DNA containing a concatenated tandem array of the consensus TFREs (catTFRE) for the majority of TF families. By using catTFRE to enrich TFs from cells, we were able to identify as many as 400 TFs from a single cell line and a total of 878 TFs from 11 cell types, covering more than 50% of the gene products that code for the DNA-binding TFs in the genome. We further demonstrated that catTFRE pull-downs could quantitatively measure proteome-wide changes in DNA binding activity of TFs in response to exogenous stimulation by using a label-free MS-based quantification approach. Applying catTFRE on the evaluation of drug effects, we described a panoramic view of TF activations and provided candidates for the elucidation of molecular mechanisms of drug actions. We anticipate that the catTFRE affinity strategy will find widespread applications in biomedical research.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Cell Line
  • Chromatography, Liquid
  • Computational Biology
  • DNA / metabolism*
  • DNA Primers / genetics
  • Gene Expression Regulation / drug effects
  • Gene Expression Regulation / genetics*
  • Humans
  • Protein Array Analysis / methods*
  • Proteome / genetics*
  • Response Elements / genetics*
  • Tandem Mass Spectrometry
  • Transcription Factors / genetics*
  • Transcription Factors / isolation & purification*
  • Transcription Factors / metabolism


  • DNA Primers
  • Proteome
  • Transcription Factors
  • DNA