The RNA exosome maintains cellular RNA homeostasis by controlling transcript abundance in the brain

Intracellular ribonucleases (RNases) are essential in all aspects of RNA metabolism, including maintaining accurate RNA levels. Inherited mutations in genes encoding ubiquitous RNases are associated with human diseases, primarily affecting the nervous system. Recessive mutations in genes encoding an evolutionarily conserved RNase complex, the RNA exosome, lead to syndromic neurodevelopmental disorders characterized by progressive neurodegeneration, such as Pontocerebellar Hypoplasia Type 1b (PCH1b). We establish a CRISPR/Cas9-engineered Drosophila model of PCH1b to study cell-type-specific post-transcriptional regulatory functions of the nuclear RNA exosome complex within fly head tissue. Here, we report that pathogenic RNA exosome mutations alter activity of the complex, causing widespread dysregulation of brain-enriched cellular transcriptomes, including rRNA processing defects—resulting in tissue-specific, progressive neurodegenerative effects in flies. These findings provide a comprehensive understanding of RNA exosome function within a developed animal brain and underscore the critical role of post-transcriptional regulatory machinery in maintaining cellular RNA homeostasis within the brain. Overall design: Two biological replicates of newly eclosed adult female flies were prepared for each biological replicate (Rrp40WT, Rrp40G11A, and Rrp40G146C). For each sample, 20 fly heads were pooled together, and nuclei were dissociated. Nuclei quantity and and quality were determined using propidium iodide. Single-cell libraries were prepared using Chromium Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.1. Sequencing reads were mapped to the Drosophila melanogaster genome and CellRanger was used to create the reference.