Evolution of the essential gene <i>MN1</i> during the macroevolutionary transition toward 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 coevolution 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 <i>MN1</i> 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 the vertebrate <i>MN1</i> gene evolved from an ancestral deuterostome sequence. In vertebrates, the <i>MN1</i> gene structure, synteny, and spatiotemporal expression pattern are remarkably conserved, indicating that the gene carries out a core function. Using a newly generated mouse knock-out model, we demonstrate in vivo that <i>Mn1</i> integrated into an ancient molecular machinery and controls the expression of the <i>Cyp26</i> genes in the developing hindbrain, thereby tuning the retinoic acid levels and patterning of the developing central nervous system. This study thus showcases the emergence of a novel gene function from an ancestral sequence and its role in generating a macroevolutionary innovation. The data expand our knowledge of brain and skull codevelopment and coevolution and highlight the role of this regulatory loop in craniofacial human syndromes.