Non-consensus GLI binding sites in Hedgehog target gene regulation

BMC Mol Biol. 2010 Jan 13;11:2. doi: 10.1186/1471-2199-11-2.


Background: The GLI transcription factors, mediators of the hedgehog signal bind with high affinity to the consensus sequence GACCACCCA. The affinity of variant single substitutions in GLI binding sites has been measured systematically, but the affinities of the variant binding sites appears low compared to the frequency of occurrence of variant sites in known GLI target gene promoters.

Results: We quantified transcriptional activation by GLI using PTCH1 promoter based luciferase reporters containing all single substitutions of the GLI consensus binding site. As expected variants with very low affinity did not activate the reporter. Many lower affinity binding sequences are, however, functional in the presence of moderate GLI concentration. Using two natural non-consensus GLI site promoters we showed that substitution of the variant sequences by consensus leads to comparable activity.

Conclusions: Variant GLI binding sites with relatively low affinity can within natural promoters lead to strong transcriptional activation. This may facilitate the identification of additional direct GLI target genes.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Base Sequence
  • Binding Sites
  • Cell Line
  • Consensus Sequence
  • Hedgehog Proteins / metabolism*
  • Humans
  • Luciferases / genetics
  • Luciferases / metabolism
  • Patched Receptors
  • Patched-1 Receptor
  • Promoter Regions, Genetic
  • Receptors, Cell Surface / genetics
  • Transcription Factors / metabolism*
  • Transcriptional Activation*
  • Zinc Finger Protein GLI1


  • GLI1 protein, human
  • Hedgehog Proteins
  • PTCH1 protein, human
  • Patched Receptors
  • Patched-1 Receptor
  • Receptors, Cell Surface
  • Transcription Factors
  • Zinc Finger Protein GLI1
  • Luciferases