Dis3l2-Mediated RNA Surveillance and Extracellular Vesicle Packaging Prevent Innate Immune Activation by Aberrant Cellular RNAs [RNA-seq]

Although most efforts to understand the functions of RNAs packaged in extracellular vesicles (EVs) have focused on mRNAs and miRNAs, recent studies using less-biased sequencing techniques have revealed that tRNAs and other noncoding RNAs (ncRNAs) are far more abundant. However, the extent to which EV ncRNAs resemble overall cellular RNAs and the benefits to host cells of packaging them into EVs remain unknown. Here, we purified EVs from the culture media of mouse and human cells and characterized their RNA components using high throughput sequencing and Northern blotting. We report that EVs are enriched for numerous aberrant ncRNAs, many of which contain oligouridine tails, a modification associated with degradation by Dis3l2, a cytosolic exoribonuclease that degrades defective structured ncRNAs. Both the numbers of EVs released and the fractions of tailed RNAs in EVs increase on Dis3l2 depletion, indicating that packaging of aberrant ncRNAs into EVs occurs in competition with Dis3l2 decay. Upregulation of multiple type I interferon stimulated genes (ISGs) occurs on Dis3l2 depletion, and cells treated with a neutral sphingomyelinase inhibitor that reduces exosome biogenesis also show moderate ISG upregulation, an effect that is enhanced in Dis3l2-depleted cells and accompanied by the accumulation of aberrant ncRNAs in cellular RNA. Thus, Dis3l2 degradation and packaging of aberrant RNAs into vesicles may prevent these RNAs from activating innate immune sensors and triggering an interferon response.