RNA exosome mutations in pontocerebellar hypoplasia alter ribosome biogenesis and p53 levels

The eukaryotic RNA exosome is a ubiquitously expressed complex of nine core proteins (EXOSC1-9) and associated nucleases responsible for RNA processing and degradation. Autosomal recessive mutations in EXOSC3, EXOSC8, EXOSC9 and the exosome cofactor RBM7 cause pontocerebellar hypoplasia and motor neuronopathy. To understand the importance of the exosome in neurodegeneration, we investigated the consequences of exosome mutations on RNA metabolism and cellular survival in zebrafish and human cell models. We observed that levels of mRNAs encoding p53 and ribosome biogenesis factors are upregulated in zebrafish lines with homozygous mutations of exosc8 or exosc9, respectively. In addition, exosome deficiency leads to increased levels of multiple non-coding RNAs (e.g. tRNAs, snoRNAs, scaRNAs). Consistent with higher p53 levels, mutant zebrafish have a reduced head size, smaller brain and cerebellum caused by an increased number of apoptotic cells during development. Downregulation of EXOSC9 in human cells leads to p53 protein stabilisation and G2/M cell cycle arrest. The work provides explanation for the pathogenesis of exosome-related disorders and highlights the link between exosome function, ribosome biogenesis and p53-dependent signalling. RNAseq case - control analysis of Human induced Neuronal Progenitor Cells (iNPCs) and CRISPR/cas9 Zebrafish embryos. Human fibroblasts with recessive mutations in EXOSC3, EXOSC8 or EXOSC9 and three different healthy contols were reprogrammed to iNPCs and sequenced with total RNAseq. Zebrafish embryos homozygous for CRISPR/cas9 induced mutations in exosc8 or exosc9 underwent total RNA sequencing along with three sets of non-mutant embyo controls. Sequencng was performed on three biological replicates of all samples across four lanes of an Illumina HiSeq 2500 platform.