N6-Methyladenosine in Flaviviridae Viral RNA Genomes Regulates Infection

Summary

The RNA modification N6-methyladenosine (m ⁶A) post-transcriptionally regulates RNA function. The cellular machinery that controls m ⁶A includes methyltransferases and demethylases that add or remove this modification, as well as m ⁶A-binding YTHDF proteins that promote the translation or degradation of m ⁶A-modified mRNA. We demonstrate that m ⁶A modulates infection by hepatitis C virus (HCV). Depletion of m ⁶A methyltransferases or an m ⁶A demethylase, respectively, increases or decreases infectious HCV particle production. During HCV infection, YTHDF proteins relocalize to lipid droplets, sites of viral assembly, and their depletion increases infectious viral particles. We further mapped m ⁶A sites across the HCV genome and determined that inactivating m ⁶A in one viral genomic region increases viral titer without affecting RNA replication. Additional mapping of m ⁶A on the RNA genomes of other Flaviviridae, including dengue, Zika, yellow fever, and West Nile virus, identifies conserved regions modified by m ⁶A. Altogether, this work identifies m ⁶A as a conserved regulatory mark across Flaviviridae genomes.

Graphical Abstract

Highlights

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  The RNA genomes of HCV, ZIKV, DENV, YFV, and WNV contain m ⁶A modification

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  The cellular m ⁶A machinery regulates HCV infectious particle production

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  YTHDF proteins reduce HCV particle production and localize at viral assembly sites

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  m ⁶A-abrogating mutations in HCV E1 increase infectious particle production

Abstract

N6-methyladenosine (m ⁶A) post-transcriptionally regulates RNA function. Gokhale et al. demonstrate that the RNA genomes of HCV, ZIKV, DENV, YFV, and WNV are modified by m ⁶A. Depletion of cellular machinery that regulates m ⁶A or introduction of m ⁶A-abrogating mutations within HCV RNA increase viral particle production, suggesting that m ⁶A negatively regulates HCV.