The ancient logic of HOX-TALE DNA binding predates bilaterian diversification
HOX transcription factors control the intricate regional specialization of animal body plans by deploying distinct DNA-binding specificities along the developing anterior-posterior axis. Although this regulatory logic underlies bilaterian diversification, its evolutionary origin remains unresolved. Cnidarians, the sister group to Bilateria, diverged before the extensive radiation that shaped the complex regulatory architectures of bilaterian HOX clusters. The use of protein sequence conservation to identify cnidarian HOX orthologs suggests that cnidarian genomes lack parts of the bilaterian HOX repertoire, raising the question of how the full set of HOX DNA-binding specificities arose. To address this question in the model sea anemone Nematostella vectensis, here we integrate quantitative SELEX-seq, high-resolution ChIP-nexus, and functional enhancer assays to demonstrate that cnidarian HOX DNA-binding specificities recapitulate the full repertoire present in bilaterians. We also find that some Nematostella AntHOX proteins have less restrictive specificities compared to their bilaterian counterparts. Thus, the underlying regulatory logic of HOX-mediated bilaterian axial identity specification is present in cnidarians. These findings suggest that the core features of HOX-DNA recognition were present in the last common ancestor of cnidarians and bilaterians.