Dynamics of Human and Viral RNA Methylation during Zika Virus Infection

Infection with the flavivirus Zika (ZIKV) causes neurological, immunological, and developmental defects through incompletely understood mechanisms. We report that ZIKV infection affects viral and human RNAs by altering the topology and function of N⁶-adenosine methylation (m⁶A), a modification affecting RNA structure and function. m⁶A nucleosides are abundant in ZIKV RNA, with twelve m⁶A peaks identified across full-length ZIKV RNA. m⁶A in ZIKV RNA is controlled by host methyltransferases METTL3 and METTL14 and demethylases ALKBH5 and FTO, and knockdown of methyltransferases increases, while silencing demethylases decreases, ZIKV production. YTHDF family proteins, which regulate the stability of m⁶A-modified RNA, bind to ZIKV RNA, and their silencing increases ZIKV replication. Profiling of the m⁶A methylome of host mRNAs reveals that ZIKV infection alters m⁶A location in mRNAs, methylation motifs, and target genes modified by methyltransferases. Our results identify a mechanism by which ZIKV interacts with and alters host cell functions.