35The RNA modification N6-methyladenosine (m 6 A) can modulate mRNA fate and thus 36 affect many biological processes. We analyzed m 6 A modification across the transcriptome 37 following infection by dengue virus (DENV), Zika virus (ZIKV), West Nile virus (WNV), and 38 hepatitis C virus (HCV). We found that infection by these viruses in the Flaviviridae family alters 39 m 6 A modification of specific cellular transcripts, including RIOK3 and CIRBP. During viral 40 infection, the addition of m 6 A to RIOK3 promotes its translation, while loss of m 6 A in CIRBP 41 promotes alternative splicing. Importantly, we found that activation of innate immune sensing or 42 the endoplasmic reticulum (ER) stress response by viral infection contributes to the changes in 43 m 6 A modification in RIOK3 and CIRBP, respectively. Further, several transcripts with infection-44 altered m 6 A profiles, including RIOK3 and CIRBP, encode proteins that influence DENV, ZIKV, 45 and HCV infection. Overall, this work reveals that cellular signaling pathways activated during 46 viral infection lead to alterations in m 6 A modification of host mRNAs to regulate infection. 47 48 Introduction 49