N6-Methyladenosine in Flaviviridae Viral RNA Genomes Regulates Infection

• Type of Material: Article
• Authors: Nandan S. Gokhale, Duke University; Alexa B.R. McIntyre, Weill Cornell Medicine; Michael J. McFadden, Duke University; Allison E. Roder, Duke University; Edward M. Kennedy, Duke University; Jorge A. Gandara, Weill Cornell Medicine; Sharon E. Hopcraft, Icahn School of Medicine at Mount Sinai; Kendra M. Quicke, Emory University; Christine Vazquez, Duke University; Jason Willer, Duke University; Olga R. Ilkayeva, Duke University; Brittany A. Law, Duke University; Christopher L. Holley, Duke University; Mariano A. Garcia-Blanco, University of Texas Medical Branch; Matthew J. Evans, Icahn School of Medicine at Mount Sinai; Mehul Suthar, Emory University; Shelton S. Bradrick, University of Texas Medical Branch; Christopher E. Mason, Weill Cornell Medicine; Stacy M. Horner, Duke University
• Language: English
• Date: 2016-11-09
• Publisher: Elsevier (Cell Press)
• Publication Version: Final Published Version
• Copyright Statement: © 2016 The Authors
• License: Creative Commons Attribution 4.0 International
• Final Published Version (URL): http://dx.doi.org/10.1016/j.chom.2016.09.015
• Title of Journal or Parent Work: Cell Host and Microbe
• ISSN: 1931-3128
• Volume: 20
• Issue: 5
• Start Page: 654
• End Page: 665
• Grant/Funding Information: Additional funding sources were the Duke Whitehead Scholarship (S.M.H.), the Ford Foundation (C.V.), the Tri-Institutional Training Program in Computational Biology and Medicine (A.B.R.M.), STARR (I7-A765 and I9-A9-071; C.E.M.), the Irma T. Hirschl and Monique Weill-Caulier Charitable Trusts, the Bert L. and N. Kuggie Vallee Foundation, WorldQuant, the Pershing Square Sohn Cancer Research Alliance, NASA (NNX14AH50G and 15-15Omni2-0063), the Bill and Melinda Gates Foundation (OPP1151054), and the Alfred P. Sloan Foundation (G-2015-13964), the U-TX STARs Award (M.A.G.-B.), UTMB (M.A.G.-B. and S.S.B.), Pew Charitable Trusts (USPHS-AI07647 and ACS-RSG-12-176-01-MPC; M.J.E.), and the Burroughs Wellcome Fund.; This work was supported by funds from the NIH: R01AI125416 (S.M.H. and C.E.M.); 5P30AI064518 (S.M.H.); T32-CA009111 (A.E.R.); R25EB020393, R01NS076465, and R01ES021006 (C.E.M.); R01AI089526 and R01AI101431 (M.A.G.-B.); R01DK0951250 (M.J.E.); and U19AI083019 and R56AI110516 (M.S.S.).
• Keywords: REVEALS; Parasitology; Microbiology; Science & Technology; N-6-METHYLADENOSINE; Life Sciences & Biomedicine; TRANSLATIONAL CONTROL; PROTEIN; SITES; Virology; HOST FACTORS; METHYLATION; GENE-EXPRESSION REGULATION; HEPATITIS-C VIRUS; SEQUENCE SPECIFICITY
• Research Categories: Biology, Genetics; Biology, Microbiology

Abstract

The RNA modification N6-methyladenosine (m6A) post-transcriptionally regulates RNA function. The cellular machinery that controls m6A includes methyltransferases and demethylases that add or remove this modification, as well as m6A-binding YTHDF proteins that promote the translation or degradation of m6A-modified mRNA. We demonstrate that m6A modulates infection by hepatitis C virus (HCV). Depletion of m6A methyltransferases or an m6A demethylase, respectively, increases or decreases infectious HCV particle production. During HCV infection, YTHDF proteins relocalize to lipid droplets, sites of viral assembly, and their depletion increases infectious viral particles. We further mapped m6A sites across the HCV genome and determined that inactivating m6A in one viral genomic region increases viral titer without affecting RNA replication. Additional mapping of m6A on the RNA genomes of other Flaviviridae, including dengue, Zika, yellow fever, and West Nile virus, identifies conserved regions modified by m6A. Altogether, this work identifies m6A as a conserved regulatory mark across Flaviviridae genomes.