5-Methylcytosine (m5C) is a widespread post-transcriptional RNA modification and is reported to be involved in manifold cellular responses and biological processes through regulating
RNA metabolism. However, its regulatory role in
antiviral innate immunity has not yet been elucidated. Here, we report that NSUN2, a typical
m5C methyltransferase, negatively regulates
type I interferon responses during various
viral infections, including SARS-CoV-2. NSUN2 specifically mediates m5C methylation of IRF3
mRNA and accelerates its degradation, resulting in low levels of IRF3 and downstream IFN-β production. Knockout or knockdown of NSUN2 enhanced
type I interferon and downstream ISGs during various
viral infection in vitro. And in vivo, the
antiviral innate response is more dramatically enhanced in Nsun2+/- mice than in Nsun2+/+ mice. The highly m5C methylated cytosines in IRF3
mRNA were identified, and their mutation enhanced cellular IRF3
mRNA levels. Moreover,
infection with Sendai virus (SeV),
vesicular stomatitis virus (VSV), herpes simplex virus 1 (HSV-1), or Zika virus (ZIKV) resulted in a reduction of endogenous NSUN2 levels. Especially,
SARS-CoV-2 infection (WT strain and
BA.1 omicron variant) also decreased endogenous levels of NSUN2 in
COVID-19 patients and K18-hACE2 KI mice, further increasing
type I interferon and downstream ISGs. Together, our findings reveal that NSUN2 serves as a negative regulator of
interferon response by accelerating the fast turnover of IRF3
mRNA, while endogenous NSUN2 levels decrease during SARS-CoV-2 and various
viral infections to boost
antiviral responses for effective elimination of viruses.