Global loss of cellular m ⁶ A RNA methylation following infection with different SARS-CoV-2 variants

Abstract

Insights into host-virus interactions during SARS-CoV-2 infection are needed to understand COVID-19 pathogenesis and may help to guide the design of novel antiviral therapeutics. <i>N</i> ⁶-Methyladenosine modification (m⁶A), one of the most abundant cellular RNA modifications, regulates key processes in RNA metabolism during stress response. Gene expression profiles observed postinfection with different SARS-CoV-2 variants show changes in the expression of genes related to RNA catabolism, including m⁶A readers and erasers. We found that infection with SARS-CoV-2 variants causes a loss of m⁶A in cellular RNAs, whereas m⁶A is detected abundantly in viral RNA. METTL3, the m⁶A methyltransferase, shows an unusual cytoplasmic localization postinfection. The B.1.351 variant has a less-pronounced effect on METTL3 localization and loss of m⁶A than did the B.1 and B.1.1.7 variants. We also observed a loss of m⁶A upon SARS-CoV-2 infection in air/liquid interface cultures of human airway epithelia, confirming that m⁶A loss is characteristic of SARS-CoV-2-infected cells. Further, transcripts with m⁶A modification are preferentially down-regulated postinfection. Inhibition of the export protein XPO1 results in the restoration of METTL3 localization, recovery of m⁶A on cellular RNA, and increased mRNA expression. Stress granule formation, which is compromised by SARS-CoV-2 infection, is restored by XPO1 inhibition and accompanied by a reduced viral infection in vitro. Together, our study elucidates how SARS-CoV-2 inhibits the stress response and perturbs cellular gene expression in an m⁶A-dependent manner.