The specification of cell types in the ventral half of the mouse neural tube depends on graded activity of the Sonic hedgehog (Shh) signaling pathway. Recent results demonstrated that Intraflagellar transport (IFT) proteins are required for the specification of Shh-dependent ventral neural cell types. IFT proteins are required for the production of cilia, and cilia appear to act as organelles that are required for cells to respond to Shh signals. Genetic and biochemical experiments will establish whether the activity of two components of the Shh pathway that act between Smo and Gli proteins, Sufu and PKA, depend on cilia. Experiments will test whether specific IFT proteins, Dnchc2 and IFT172, have unique functions in Hh signaling. Genetic experiments will test whether Dnchc2 defines differences in the mechanism of Hh signaling along the anterior-posterior body axis. Biochemical experiments will test whether IFT172 has a dual function in the cilium and in the nucleus. Experiments will test whether cilia are required for two other signaling pathways important in neural development, Pdgf and non-canonical Wnt signaling, and whether cilia act as sites for signal integration. The hypothesis that the basal body acts as a signaling center during neural patterning will be tested by examining the phenotypes of key basal body components, using existing gene trap mutations. New ENU-mutations that affect the specification of motor neurons will be characterized. Because of the important roles of abnormal Hh signaling in birth defects and cancer, the characterization of mammalian-specific components of the Hh pathway has important implications for human health. These mammalian-specific components of the pathway may be mutated in human congenital disorders and in human tumors. The new components may also provide novel drug targets for treatment of disorders associated with abnormal Hh signaling. A large number of human congenital disorders have recently been connected to defects in cilia. These studies will help define which of the phenotypes associated with these syndromes are the result of inappropriate signaling by the Hh and other signaling pathways.