Genetic architecture of craniofacial morphogenesis: roles of PAX3, PAX7, and PAX9

Craniofacial morphogenesis is a highly coordinated developmental process governed by complex genetic and molecular interactions. Among these, the PAX family of transcription factors plays a pivotal role in the regulation of neural crest specification, mesenchymal differentiation, and skeletal patterning. This review highlights the distinct and overlapping roles of PAX3, PAX7, and PAX9 in craniofacial development, focusing on their gene regulatory networks, developmental mechanisms, and clinical implications. PAX3 and PAX7 orchestrate neural crest and cranial mesodermal pathways, whereas PAX9 controls odontogenesis and skeletal morphogenesis. We also discuss emerging insights from systems biology, organoid models, and comparative genomics that advance our understanding of PAX-driven facial morphogenesis and its relevance to congenital craniofacial disorders.