MeRIP-seq for host response to Flaviviridae infection

The modification N6-methyladenosine (m6A) affects rates of translation and degradation of mRNA transcripts. We analyzed m6A across the transcriptome following infection by dengue virus (DENV), Zika virus (ZIKV), West Nile virus (WNV), and hepatitis C virus (HCV) using MeRIP-seq. We used the uninfected replicates, among which we would expect little biological variation in methylation, as negative controls to validate statistical methods for the detection of m6A changes in MeRIP-seq data. Applying validated statistical methods, we found that innate immune response to Flaviviridae viruses alters m6A modification of specific cellular transcripts compared to uninfected controls. Finally, we find that these changes in m6A can in turn affect splicing or translation of genes relevant to infection. 3 replicates for each virus (DENV, HCV, WNV, and ZIKV) were generated, with IP (anti-m6A antibody, NEB) and input samples for each. RNA was extracted from Huh7 cells at 48 hours post infection. Uninfected samples were sequenced for comparison, with 3 replicates per lab of incubation (mockL - matched to WNV, and mockH - matched to DENV, HCV, and ZIKV) and two time points, early (mocks at 16 or 24 hours) and late (mocks and viruses at 48 hours).