Evolution of the essential gene MN1 during the macroevolutionary transition towards patterning the vertebrate hindbrain

The tight link between brain and skull formation is a fundamental aspect of vertebrate evolution and embryogenesis. Their developmental synchronization is essential for structural and functional integration. The brain and skull shape co-evolution is evident along the vertebrate phylogeny, however, the genetic basis underlying their close evolutionary and developmental relationship remains little explored. Here, we reveal the evolution and function of the MN1 gene that was previously found to be associated with significant shape variation in the mouse skull and the formation of cranial bones. We show that MN1 is a taxon-restricted gene that emerged in the common ancestor of vertebrates. The MN1 gene structure, synteny and spatiotemporal expression pattern are remarkably conserved across gnathostomes, indicating that the gene is under strong purifying selection and carries out a core function. Based on a knock-out model, we demonstrate in vivo that Mn1 integrated into an ancient molecular machinery and controls the expression of the Cyp26 genes in the developing hindbrain, thereby tuning the retinoic acid levels and patterning of the emerging nervous system. This study shows the essential role of a taxon-restricted gene in generating a macroevolutionary innovation, expands our knowledge of brain and skull co-development and co-evolution and highlights the role of this new regulatory loop in craniofacial human syndromes.