Mott, J.; Pei, Z.; Sun, J.; Lee, C. H.; Puri, T.; Sachs, Z. M.; Aviles Vargas, A.; Blaha, N.; Tong, M.; Liu, A.; Wang, Y.; Kim, Y.; Girirajan, S.; Zhang, J.; Mao, Y.

RNA-Binding Motif Protein 8A (RBM8A) is a core component of the exon junction complex (EJC), which plays a fundamental role in post-transcriptional RNA regulation. Mutations in the RBM8A gene cause thrombocytopenia-absent radius (TAR) syndrome, characterized by reduced platelet number and radial defects. However, how its function contributes to bone development remains poorly understood. We found that RBM8A is highly expressed in human bone marrow-derived mesenchymal stem cells (MSCs) and mouse embryonic limb buds. To further investigate the role of RBM8A in bone development, we generated an Rbm8a conditional knockout mouse (cKO) model in the early limb bud and craniofacial mesenchyme using the Prx1-cre line, which recapitulates key features of TAR syndrome. Rbm8a deficiency in this mouse model resulted in significant defects in limb and craniofacial development, including shorter limb bones across developmental timepoints, delayed ossification, altered cranial morphogenesis, along with impairments in motor function and reduced brain size. To elucidate the molecular basis of these phenotypes, we performed RNA immunoprecipitation sequencing (RIP-seq) in embryonic limb tissue. Our analysis revealed that RBM8A preferentially associates with long, exon-rich transcripts with high isoform complexity. These transcripts are enriched in pathways related to primary cilia, RNA processing, and developmental signaling. Consistent with this, transcriptomic and enrichment analyses identified strong associations with ciliopathy-related and congenital skeletal disease gene sets. At the cellular level, Rbm8a deficiency resulted in altered expression of key chondrogenic and ossification markers in embryonic limb bone tissue, such as reduced SOX9 and increased IHH in the primary ossification center, suggesting impaired progression of endochondral ossification and disrupted Hedgehog pathway activity. Quantitative Reverse Transcription PCR (qRT-PCR) analysis further validated selective downregulation of Hedgehog pathway targets, including Gli3 and Hhip, while other developmental genes remained unchanged, indicating pathway-specific attenuation. Together, these findings support a model in which Rbm8a regulates structurally complex transcripts that are enriched in ciliary and developmental signaling pathways, and that disruption of this process leads to selective impairment of Hedgehog signaling and skeletal development. These results provide a novel mechanistic link between RNA processing and developmental signaling and offer new insight into how defects in RNA regulation contribute to congenital skeletal abnormalities.