Factors downstream of Shh signalling in gill arch and branchial ray development in the little skate

In the tetrapod limb bud, Shh from the ZPA functions initially as a morphogen to establish the anteroposterior axis of the limb, and subsequently as a mitogen to maintain proliferative expansion of limb endoskeletal progenitors, the latter via a positive feedback loop between ZPA Shh and AER Fgf signalling. ZPA-AER feedback is mediated by bone morphogenetic protein (Bmp) signalling: Bmp from the distal limb bud negatively regulates AER function, but this effect is tempered by Shh-induced expression of the secreted Bmp antagonist gremlin. Previously, the Gillis lab has shown that, as in the limb bud, skate GAER Shh signalling functions initially to establish the anteroposterior axis of the gill arch, and subsequently to maintain proliferative expansion of branchial ray progenitors (likely via maintenance of Fgf signalling). However, the downstream molecular effectors in branchial ray axial patterning remain poorly understood. This project contains RNA-seq libraries from a differential gene expression experiment where the transcriptomic profiles of control (DMSO treated) and hedgehog-inhibited (cyclopamine treated) skate gill arches (gill arch 1/pharyngeal arch 3 dissected out) were compared at stages 22 and 25.