miR-122 Stimulates Hepatitis C Virus RNA Synthesis by Altering the Balance of Viral RNAs Engaged in Replication versus Translation

The liver-specific microRNA, miR-122, stabilizes hepatitis C virus (HCV) RNA genomes by recruiting host argonaute 2 (AGO2) to the 5′ end and preventing decay mediated by exonuclease Xrn1. However, HCV replication requires miR-122 in Xrn1-depleted cells, indicating additional functions. We show that miR-122 enhances HCV RNA levels by altering the fraction of HCV genomes available for RNA synthesis. Exogenous miR-122 increases viral RNA and protein levels in Xrn1-depleted cells, with enhanced RNA synthesis occurring before heightened protein synthesis. Inhibiting protein translation with puromycin blocks miR-122-mediated increases in RNA synthesis, but independently enhances RNA synthesis by releasing ribosomes from viral genomes. Additionally, miR-122 reduces the fraction of viral genomes engaged in protein translation. Depleting AGO2 or PCBP2, which binds HCV RNA in competition with miR-122 and promotes translation, eliminates miR-122 stimulation of RNA synthesis. Thus, by displacing PCBP2, miR-122 reduces HCV genomes engaged in translation while increasing the fraction available for RNA synthesis. [Display omitted] •miR-122 promotes HCV replication independently of protecting HCV RNA from Xrn1•miR-122 stimulates HCV RNA synthesis prior to promoting viral protein synthesis•Stimulation of RNA synthesis requires active protein translation, AGO2, and PCBP2•miR-122 displaces PCBP2 to rebalance RNA engagement in RNA versus protein synthesis miR-122 is an important host factor for HCV, acting in part by protecting its genome from Xrn1-mediated decay. Masaki et al. show miR-122 also directly stimulates viral RNA synthesis by competing with PCBP2 for binding to the RNA and increasing the fraction of viral RNAs engaged in replication versus translation.