Enzymolysis-based RNA pull-down identifies YTHDC2 as an inhibitor of antiviral innate response
Jun Zhu, Shuo Liu, Jiali Fang, Zenghui Cui, Bingjing Wang, Yuzhou Wang, Lin Liu, Qingqing Wang, Xuetao Cao
Abstract
The innate immune response must be terminated in a timely manner at the late stage of infection to prevent unwanted inflammation. The role of m 6 A-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 m 6 A-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 m 6 A-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.