N6-methyladenosine (m 6 A) RNA modifications control the antiviral response to influenza A virus infection by limiting IFITM2/3 expression

ABSTRACT N 6 -methyladenosine (m 6 A) RNA modifications regulate diverse cellular processes, including the response to virus infection. However, how m 6 A controls antiviral gene expression and whether effects on viral replication are due to direct modification of viral RNA or regulation of cellular transcripts remain unclear. Herein, we analysed how m 6 A modifications control the cell-autonomous innate immune response to influenza A virus (IAV) infection. Depletion or inhibition of the m 6 A writer METTL3 or the m 6 A reader YTHDF2 restricts IAV replication. However, using a quantitative method to identify m 6 A sites, we did not detect substantial m 6 A modification of viral RNA. In contrast, many IAV-induced cellular transcripts were m 6 A modified in their coding region, including those that encode pattern recognition receptors and direct antiviral proteins. Inhibition of interferon signalling restored IAV replication after METTL3 inhibition, highlighting that m 6 A controls the antiviral response to infection. METTL3 inhibition increased expression of the paralogous antiviral proteins IFITM2 and IFITM3, which were required for the antiviral activity of the METTL3 inhibitor. We propose that m 6 A modifications regulate the expression of antiviral proteins to limit the magnitude of their induction and balance antiviral activity with maintaining cellular homeostasis.