Proposed model for role of Pax9-mediated signalling during pharyngeal arch artery development. (A) In wild-type embryos, Pax9 expression in the 3rd pharyngeal arch endoderm induces neural crest cells (NCCs), either directly or indirectly, to differentiate into the SMCs that form around the endothelium of the remodelling 3rd PAAs. In the 4th arch endoderm, Tbx1 and Pax9 function together to, most likely indirectly, control formation of the 4th PAAs, potentially through collaboration with Chd7 and Gbx2. (B) In Pax9-deficient embryos, signals from the 3rd pharyngeal arch endoderm are compromised and NCC differentiation into SMCs is impaired, resulting in the collapse of the 3rd PAAs by E11.5. In Tbx1-Pax9 double heterozygous embryos, reduced levels of Tbx1 and Pax9 in the 4th pharyngeal arch endoderm are insufficient to allow the 4th PAAs to form.