Global loss of cellular m⁶A RNA methylation following infection with different SARS-CoV-2 variants

Abstract

Host-viral interactions during SARS-CoV-2 infection are needed to understand COVID-19 pathogenesis and may help to guide the design of novel antiviral therapeutics. N6-methyladenosine modification (m6A), one of the most abundant cellular RNA modifications, regulates key processes in RNA metabolism during a stress response. Gene expression profiles observed post-infection 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 caused a loss of m6A in cellular RNAs, whereas m6A was detected abundantly in viral RNA. METTL3, the m6A methyltransferase, showed an unusual cytoplasmic localization post-infection. The B.1.351 variant had a less pronounced effect on METTL3 localization and loss of m6A than 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 were preferentially down-regulated post-infection. Inhibition of the export protein XPO1 resulted in the restoration of METTL3 localization, recovery of m6A on cellular RNA, and increased mRNA expression. Stress granule formation, which was compromised by SARS-CoV-2 infection, was 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.

METTL3/MYCN cooperation drives neural crest differentiation and provides therapeutic vulnerability in neuroblastoma

“…This fragmented RNA was either used for RNA-seq or m 6 A RIP-seq. m 6 A RIP was performed as previously described (5,19,25) with m 6 A antibody. Input and m 6 A RIP RNA were used to generate sequencing libraries using SMARTer Stranded Total RNA-Seq kit V2, Pico Input Mammalian (Takara Bio).…”

“…m 6 A is deposited on cellular RNA cotranscriptionally by the enzyme complex METTL3/METTL14/WTAP (1). A role for m 6 A RNA modification has been shown in chromatin regulation, stress response, DNA damage repair, as well as in viral infection by regulating gene expression both at transcriptional and post-transcriptional levels (2)(3)(4)(5). Active chromatin modification H3K36me3, RNA binding proteins such as RBFOX2, and transcription factors have been implicated in METTL3 recruitment (6)(7)(8).…”