Retinoic acid-responsive hox genes in hoxba and hoxbb clusters direct pharyngeal pouch formation in zebrafish

The segmented pharyngeal apparatus is crucial for organ development specific to vertebrates, and its formation relies on the proper development of pharyngeal pouches. While retinoic acid (RA) is known to influence pouch formation, the downstream genes involved have been unclear. In this study, we demonstrate that zebrafish mutants lacking both the hoxba and hoxbb clusters—teleost-specific duplicates of the ancestral HoxB cluster—exhibit a significant loss of posterior pharyngeal pouches and related skeletal elements. This phenotype resembles that observed in raldh2 and pax1a;pax1b mutants. We identify hoxb1a and hoxb1b as RA-dependent genes expressed in the pharyngeal region that are essential for pouch formation. Morpholino-mediated knockdown of these genes replicated the pouch defects and decreased pax1a expression, indicating a regulatory pathway linking RA, Hox , and pax1 . Our findings uncover a previously unrecognized role of Hox genes in early pouch segmentation and suggest that RA-responsive HoxB clusters were co-opted during vertebrate evolution to initiate pharyngeal regionalization.