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
Affiliations
Jun Zhu
Institute of Immunology, Zhejiang University School of Medicine, Hangzhou 310058, China; Frontier Research Center for Cell Response, Institute of Immunology, College of Life Sciences, Nankai University, Tianjin 300071, China
Shuo Liu
Department of Immunology, Institute of Basic Medical Sciences, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100005, China
Jiali Fang
Frontier Research Center for Cell Response, Institute of Immunology, College of Life Sciences, Nankai University, Tianjin 300071, China
Zenghui Cui
Frontier Research Center for Cell Response, Institute of Immunology, College of Life Sciences, Nankai University, Tianjin 300071, China
Bingjing Wang
Department of Immunology, Institute of Basic Medical Sciences, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100005, China
Yuzhou Wang
Department of Cell Biology and Genetics, College of Life Sciences, Nankai University, Tianjin 300071, China
Lin Liu
Department of Cell Biology and Genetics, College of Life Sciences, Nankai University, Tianjin 300071, China
Qingqing Wang
Institute of Immunology, Zhejiang University School of Medicine, Hangzhou 310058, China
Xuetao Cao
Institute of Immunology, Zhejiang University School of Medicine, Hangzhou 310058, China; Frontier Research Center for Cell Response, Institute of Immunology, College of Life Sciences, Nankai University, Tianjin 300071, China; Department of Immunology, Institute of Basic Medical Sciences, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100005, China; Chinese Academy of Medical Sciences Oxford Institute, Chinese Academy of Medical Sciences, Beijing 100005, China; Corresponding author
Summary: 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.
