Transcriptional regulation of sonic hedgehog target genes in the mammalian limb

The Hedgehog (HH) family of secreted proteins are critical regulators of embryonic development. Dysregulation of the HH pathway results in a large class of developmental defects as well as several types of cancer. HH signaling elicits a transcriptional response by regulating GLI transcription factors. The mechanisms by which GLIs activate and sustain gene expression in response to HH are not well understood. To address this in the limb, we undertook a systems level analysis to determine the spatiotemporal kinetics of the GLI transcriptional response. In addition, we focus on the regulation of a single GLI-bound cis-regulatory module (CRM) associated with the GLI target gene, Gremlin. And lastly, we establish a primary limb cell culture method that can be utilized in a medium throughput manner to manipulate gene expression and test the activity of DNA elements. This work provides the first characterization of the spatiotemporal response of a large group of GLI target genes. Furthermore, this work lays the foundation for a systems-level understanding of the gene regulatory networks underlying SHH-mediated limb patterning.