Cis-regulatory modules in the mammalian liver: composition depends on strength of Foxa2 consensus site

Nucleic Acids Res. 2008 Jul;36(12):4149-57. doi: 10.1093/nar/gkn366. Epub 2008 Jun 13.


Foxa2 is a critical transcription factor that controls liver development and plays an important role in hepatic gluconeogensis in adult mice. Here, we use genome-wide location analysis for Foxa2 to identify its targets in the adult liver. We then show by computational analyses that Foxa2 containing cis-regulatory modules are not constructed from a random assortment of binding sites for other transcription factors expressed in the liver, but rather that their composition depends on the strength of the Foxa2 consensus site present. Genes containing a cis-regulatory module with a medium or weak Foxa2 consensus site are much more liver-specific than the genes with a strong consensus site. We not only provide a better understanding of the mechanisms of Foxa2 regulation but also introduce a novel method for identification of different cis-regulatory modules involving a single factor.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Animals
  • Base Sequence
  • Binding Sites
  • Chromatin Immunoprecipitation
  • Computational Biology
  • Consensus Sequence
  • Genomics
  • Hepatocyte Nuclear Factor 3-beta / metabolism*
  • Liver / metabolism*
  • Mice
  • Regulatory Elements, Transcriptional*
  • Transcription Factors / metabolism


  • Foxa2 protein, mouse
  • Transcription Factors
  • Hepatocyte Nuclear Factor 3-beta