The downstream targets that are activated in response to Shh pose another challenge.
 Genes that are targets of Shh signaling encode factors that lead to the formation of the autopod, stylopod and zeugopod.

Activation of Gli zinc-finger transcription factors occurs through the Hedgehog signaling pathway.
 There are three Gli factors that are essential for limb development: Gli1, Gli2 and Gli3.
 Without Shh, Gli2 and Gli3 are processed to a repressor form and travel to the nucleus to repress the Shh response.
 But when Shh is present, unprocessed Gli2 and Gli3 are able to pass into the nucleus and stimulate expression of Shh target genes, including Gli1.
  Studies in mice show that Gli3 knockouts have polydactyly digits.
Fundamentally, Shh acts to remove repression of Gli3.
 When Shh diffuses from the ZPA, it predominates in the posterior region of the limb bud, activating Gli3 in the posterior region, while the repressor is still active in the anterior region.
 This leads to activation of other genes such as Hox genes, FGF genes and BMP genes in the posterior region, setting up digit patterning.
BMP, plays a role in limb morphology, specifically, digit positioning, but the specific regulation of BMP is unclear.

In particular, the Hox genes A and D are likely to be controlled by Shh within the ZPA.
Three phases of activation of the Hox genes results in patterning of the limb parallel to the expression of the Hox genes in a nested pattern.
Activation of these genes results in a new limb axis that ultimately results in digit development, possibly interpreting gene expression to assign digit identity.
Overall, the molecular ZPA requires input for several signaling centers, but acts as an organizer itself, inducing anterior-posterior pattering of the chick limb bud.
The downstream targets that are activated in response to Shh pose another challenge.  Genes that are targets of Shh signaling encode factors that lead to the formation of the autopod, stylopod and zeugopod.
Activation of Gli zinc-finger transcription factors occurs through the Hedgehog signaling pathway.  There are three Gli factors that are essential for limb development: Gli1, Gli2 and Gli3.  Without Shh, Gli2 and Gli3 are processed to a repressor form and travel to the nucleus to repress the Shh response.  But when Shh is present, unprocessed Gli2 and Gli3 are able to pass into the nucleus and stimulate expression of Shh target genes, including Gli1.   Studies in mice show that Gli3 knockouts have polydactyly digits. Fundamentally, Shh acts to remove repression of Gli3.  When Shh diffuses from the ZPA, it predominates in the posterior region of the limb bud, activating Gli3 in the posterior region, while the repressor is still active in the anterior region.  This leads to activation of other genes such as Hox genes, FGF genes and BMP genes in the posterior region, setting up digit patterning. BMP, plays a role in limb morphology, specifically, digit positioning, but the specific regulation of BMP is unclear.
In particular, the Hox genes A and D are likely to be controlled by Shh within the ZPA. Three phases of activation of the Hox genes results in patterning of the limb parallel to the expression of the Hox genes in a nested pattern. Activation of these genes results in a new limb axis that ultimately results in digit development, possibly interpreting gene expression to assign digit identity. Overall, the molecular ZPA requires input for several signaling centers, but acts as an organizer itself, inducing anterior-posterior pattering of the chick limb bud.
Zone of polarizing activity