A bacterial one-hybrid system for determining the DNA-binding specificity of transcription factors

Nat Biotechnol. 2005 Aug;23(8):988-94. doi: 10.1038/nbt1120. Epub 2005 Jul 24.


The DNA-binding specificities of transcription factors can be used to computationally predict cis-regulatory modules (CRMs) that regulate gene expression. However, the absence of specificity data for the majority of transcription factors limits the widespread implementation of this approach. We have developed a bacterial one-hybrid system that provides a simple and rapid method to determine the DNA-binding specificity of a transcription factor. Using this technology, we successfully determined the DNA-binding specificity of seven previously characterized transcription factors and one novel transcription factor, the Drosophila melanogaster factor Odd-skipped. Regulatory targets of Odd-skipped were successfully predicted using this information, demonstrating that the data produced by the bacterial one-hybrid system are relevant to in vivo function.

Publication types

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

MeSH terms

  • Animals
  • Binding Sites
  • DNA, Bacterial / chemistry*
  • DNA, Bacterial / metabolism*
  • Drosophila Proteins / chemistry
  • Drosophila Proteins / metabolism*
  • Drosophila melanogaster
  • Escherichia coli / genetics
  • Escherichia coli / metabolism
  • Genes, Regulator
  • Protein Binding
  • Protein Interaction Mapping / methods*
  • Sensitivity and Specificity
  • Sequence Analysis / methods*
  • Transcription Factors / chemistry*
  • Transcription Factors / metabolism*
  • Two-Hybrid System Techniques*


  • DNA, Bacterial
  • Drosophila Proteins
  • Transcription Factors