Abstract Craniofacial abnormalities are some of the most commonly occurring human birth defects worldwide, with up to 200,000 children born every year with some type of craniofacial defect. These defects can occur as part of complex syndromes that involve multiple tissues and organs. The syndromic forms of these disorders have been successfully linked to nearly 500 genes including TWIST1 for craniosynostosis and IRF6 for orofacial clefting. However more frequently no other part of the body is directly involved (50% of craniosynostoses, 70% of orofacial clefts). Genome wide association studies indicate heritability for such defects, however the vast majority of associations fall outside of genes suggesting defective gene regulation is a major contributor to incidence of such defects. Gene regulatory elements can be located throughout the genome and typically have tissue-specific activity, making them difficult to identify and predict what gene they control. The overall objective of this application is to integrate epigenomic and transcriptomic data sets from early human and mouse craniofacial development from our lab as well as FaceBase to comprehensively predict regulatory element-gene interactions. Our hypothesis posits that conserved regulatory networks between human and mouse are enriched for disease relevant biology. In Aim 1 we propose to systematically identify chromatin states in human from 4.5 to 8 weeks of gestation and in mouse from embryonic days 9.5 to 15.5. In Aim 2 we propose to identify genes that are coordinately regulated in both species across these developmental windows. Finally, in Aim 3 we propose to integrate these two disparate network types to identify regulatory element-gene pairings. We will experimentally validate predicted interactions in a culture model of cranial neural crest cells using proximity-ligation coupled with immunoprecipitation. Our proposed studies will generate the most comprehensive epigenomic and transcriptomic networks in a developing human tissue and for the first time identify the conserved regulatory architecture for building the mammalian orofacial complex.