Spatiotemporal regulation of GLI target genes in the mammalian limb bud

Dev Biol. 2015 Oct 1;406(1):92-103. doi: 10.1016/j.ydbio.2015.07.022. Epub 2015 Jul 31.


GLI proteins convert Sonic hedgehog (Shh) signaling into a transcriptional output in a tissue-specific fashion. The Shh pathway has been extensively studied in the limb bud, where it helps regulate growth through a SHH-FGF feedback loop. However, the transcriptional response is still poorly understood. We addressed this by determining the gene expression patterns of approximately 200 candidate GLI-target genes and identified three discrete SHH-responsive expression domains. GLI-target genes expressed in the three domains are predominately regulated by derepression of GLI3 but have different temporal requirements for SHH. The GLI binding regions associated with these genes harbor both distinct and common DNA motifs. Given the potential for interaction between the SHH and FGF pathways, we also measured the response of GLI-target genes to inhibition of FGF signaling and found the majority were either unaffected or upregulated. These results provide the first characterization of the spatiotemporal response of a large group of GLI-target genes and lay the foundation for a systems-level understanding of the gene regulatory networks underlying SHH-mediated limb patterning.

Keywords: Cis-regulatory modules; DNA motifs; FGF; GLI; In situ hybridization; Limb development; RNAseq; Sonic hedgehog.

Publication types

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

MeSH terms

  • Animals
  • Binding Sites / genetics
  • Body Patterning / genetics
  • Body Patterning / physiology*
  • Fibroblast Growth Factors / metabolism*
  • Gene Expression Regulation, Developmental
  • Gene Regulatory Networks
  • Hedgehog Proteins / metabolism*
  • Kruppel-Like Transcription Factors / metabolism*
  • Limb Buds / cytology
  • Limb Buds / metabolism*
  • Mice
  • Mice, Transgenic
  • Nerve Tissue Proteins / metabolism*
  • Protein Binding / genetics
  • Protein Structure, Tertiary
  • Signal Transduction / physiology
  • Transcriptional Activation
  • Zinc Finger Protein Gli3


  • Gli3 protein, mouse
  • Hedgehog Proteins
  • Kruppel-Like Transcription Factors
  • Nerve Tissue Proteins
  • Shh protein, mouse
  • Zinc Finger Protein Gli3
  • Fibroblast Growth Factors