The Mutation of myomiR miR499 Impacts the Intermuscular Bones in Zebrafish

The development of intermuscular bones (IBs) in teleost fish is regulated by osteogenic genes, but the upstream signals that initiate ossification remain elusive. Given the spatiotemporal correlation between IB formation and swimming behavior, mechanical stimuli from muscle activity have been hypothesized as potential regulators. In this study, we investigated the role of the muscle-specific microRNA miR499 in this process. Using CRISPR/Cas9-generated miR499 knockout zebrafish, we demonstrated that the mutant of miR499 induces a fast-twitch muscle phenotype through the upregulation of sox6, accompanied by increased fast-myosin gene expression and fast-twitch fiber proliferation. This shift led to distinct locomotor alterations, characterized by reduced tail-beat frequency and increased stride length. Crucially, these changes resulted in delayed IB ossification onset, slower ossification rates, and simplified morphology. The total ossification area decreased by 27%. Molecular analysis revealed a downregulation of osteogenic genes in IB tissue. Our findings establish miR499 as a key regulator of a muscle–bone functional axis, where miRNA-mediated muscle fiber specification determines mechanical output that subsequently guides IB development. This work provides new insights into the mechanobiological regulation of skeletal development and identifies a promising genetic target for aquaculture breeding programs aimed at attenuated IBs.