RNA exosome-mediated RNA surveillance governs developmental timing in the human cerebellum

Defects in RNA metabolism are a defining feature of neurodevelopmental disease, yet the contribution of RNA decay pathways to human brain development remains poorly understood. Notably, mutations in genes encoding ubiquitously expressed RNA surveillance machinery often cause highly tissue-selective disease, underscoring a central paradox in human biology. The RNA exosome is a conserved ribonuclease complex long considered a housekeeping machine for RNA turnover, yet recessive mutations in genes encoding structural subunits of the complex disproportionately cause neurological disease, suggesting an instructive role in nervous system development. Here, we show that the RNA exosome regulates the temporal progression of gene expression programs during human cerebellar differentiation. Using CRISPR-engineered human cerebellar organoids modeling EXOSC3 variants, we find that RNA exosome dysfunction does not broadly alter transcript abundance, but instead disrupts transitions between developmental states. Mutant organoids exhibit persistence of early transcriptional programs, impaired maturation of Purkinje and rhombic lip-derived lineages, and altered cellular composition. These defects are accompanied by disorganized laminar architecture and reduced coordination of neuronal activity, despite preserved intrinsic excitability. More broadly, our findings suggest that defects in RNA decay represent a general mechanism underlying neurodevelopmental disease. Together, this work establishes RNA surveillance as a key determinant of developmental timing, neural identity, and disease.