Enzymolysis-based RNA pull-down identifies YTHDC2 as an inhibitor of antiviral innate response

• Published in: Cell reports (Cambridge) 2023-10, Vol.42 (10), p.113192-113192, Article 113192
• Main Authors: Zhu, Jun, Liu, Shuo, Fang, Jiali, Cui, Zenghui, Wang, Bingjing, Wang, Yuzhou, Liu, Lin, Wang, Qingqing, Cao, Xuetao
• Format: Article
• Language: English
• Subjects: CP: Immunology; immunoglobulin G-degrading enzyme; innate immunity; mRNA degradation; RNA pull-down; RNA-binding proteins; YTHDC2
• ISSN: 2211-1247; 2211-1247
• DOI: 10.1016/j.celrep.2023.113192

The innate immune response must be terminated in a timely manner at the late stage of infection to prevent unwanted inflammation. The role of m6A-modified RNAs and their binding partners in this process is not well known. Here, we develop an enzymolysis-based RNA pull-down (eRP) method that utilizes the immunoglobulin G-degrading enzyme of Streptococcus pyogenes (IdeS) to fish out m6A-modified RNA-associated proteins. We apply eRP to capture the methylated single-stranded RNA (ssRNA) probe-associated proteins and identify YT521-B homology domain-containing 2 (YTHDC2) as the m6A-modified interferon β (IFN-β) mRNA-binding protein. YTHDC2, induced in macrophages at the late stage of virus infection, recruits IFN-stimulated exonuclease ISG20 (IFN-stimulated exonuclease gene 20) to degrade IFN-β mRNA, consequently inhibiting antiviral innate immune response. In vitro and in vivo deficiency of YTHDC2 increases IFN-β production at the late stage of viral infection. Our findings establish an eRP method to effectively identify RNA-protein interactions and add mechanistic insight to the termination of innate response for maintaining homeostasis. [Display omitted] •eRP is an effective method to identify m6A-modified RNA-binding proteins•YTHDC2 is an m6A-modified IFN-β mRNA-binding protein•YTHDC2 inhibits IFN-β expression and antiviral innate response in cells and mice•YTHDC2 promotes IFN-β mRNA degradation through recruiting ISG20 The function of RNA-binding proteins in regulating antiviral innate responses remains to be clarified. Zhu et al. report an enzymolysis-based RNA pull-down method using IdeS and identify YTHDC2 as an m6A-modified IFN-β mRNA-binding protein that inhibits IFN-β expression and antiviral innate response through recruiting ISG20 in cells and mice.