Comparative single cell genomics of facial signaling centers of avian and murine embryos
Morphogens are crucial in craniofacial development, directing cellular processes that shape facial features in vertebrates. In this study, we used single-cell RNA and ATAC sequencing to investigate the genomic regulation underlying species-specific morphogen expression in mouse and chicken embryos. We identified unique expression patterns of morphogens and receptors across facial prominences in both species and predicted cellular communication between cell populations involved in facial development. Our analysis revealed highly specific morphogen expression, predominantly originating from spatially segregated regions known as signaling centers. By examining the chromatin landscape, we uncovered species-specific regulatory elements and accessibility patterns that control gene expression and facial morphogenesis. We validated candidate enhancers in vivo, demonstrating that their activity correlates with the expression of morphogen ligands in the embryonic face. This study underscores the complex and species-specific regulation of facial morphogenesis, offering insights for comparative genomics across vertebrates with distinct facial morphologies.