NSUN2-mediated m⁵C methylation of IRF3 mRNA negatively regulates type I interferon responses during various viral infections

ABSTRACT

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.

KEYWORDS:

• 5-methylcytosine
• RNA methyltransferase
• viral infections
• antiviral innate immunity
• SARS-CoV-2

Acknowledgement

We thank Dr. Yingle Liu and Dr. Mang Shi for providing BALF samples of COVID-19 patients. We thank Dr. Zheng-Li Shi for providing SARS-CoV-2, Dr. Hong-Bing Shu for providing SeV, HSV-1, VSV-GFP, Dr. Bo Zhang for providing ZIKV, Dr. Ming-Zhou Chen for providing VSV and Dr. Ying Zhu for providing A549 IFNAR1^−/− cell. We thank Dr. Yun-Gui Yang and Dr. Cheng-Peng Fan for critical advice. Author Contributions: Y.C. and H.W. conceived the research and experiments. H.W., C.Z., J.F., L.Zhang., Z.F., J.J.L., J.L.L.and M.H. performed the major experiments and analysis. Y.Y.C. and L.Zhou. participated in mice experiments. Y.W. and X.Z. helped LC-MS/MS experiments. Y.Zhou., K.L., and D.W. analysed transcriptome sequencing data. H.T., A.J., D.G. and K.X. provided critical advice. H.W. and Y.C. wrote and revised the manuscript with contributions from all other authors.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Correction Statement

This article has been corrected with minor changes. These changes do not impact the academic content of the article.

Additional information

Funding

This study was supported by grants from National Science and Technology Major Project [grant numbers 2021YFA1300801, 2021YFF0702004, 2021YFC2300702 and 2022YFC2604101], and China NSFC projects [grant number 82172243], and Special Fund for COVID-19 Research of Wuhan University. We are grateful to Beijing Taikang Yicai Foundation for their great support to this work.