Long-range identification of hepatocyte nuclear factor-3 (FoxA) high and low-affinity binding sites with a chimeric nuclease

Philippe Ruminy, Céline Derambure, Srinivasan Chandrasegaran, Jean Philippe Salier

Research output: Contribution to journalArticlepeer-review

12 Scopus citations


Identifying the complete set of transcription factors that bind the promoter and other regulatory regions of a gene of interest is an essential step in functional genomics. We have developed an original assay for the systematic detection of hepatocyte nuclear factor-3 (HNF-3) binding sites within cloned promoters. This assay is based on expression of a recombinant enzyme, HNF-3β/FN, that is comprised of the rat HNF-3β DNA-binding domain and the non-specific nuclease domain of the FokI restriction enzyme. Southern analysis of target plasmids with proven HNF-3 binding sites showed that HNF-3β/FN was able to specifically cut both DNA strands in the vicinity of these binding sites, whereas mutagenized binding sites were no longer cleaved. Likewise, as yet undescribed HNF-3 binding sites were detected easily over a distance spanning several thousand bases. The functionality of such binding sites was confirmed by electromobility shift assay. Furthermore, the extent of cleavage by HNF-3β/FN at a given binding site was tightly correlated with the affinity of a natural HNF-3β molecule for this site. This novel approach can be extended to other transcription factors for long-range identification of functional transcription factor binding sites in genes.

Original languageEnglish (US)
Pages (from-to)523-535
Number of pages13
JournalJournal of molecular biology
Issue number3
StatePublished - Jul 13 2001


  • Chimeric nuclease
  • Cleavage
  • Detection
  • Genomics
  • Transcription factor

ASJC Scopus subject areas

  • Structural Biology
  • Molecular Biology


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