N6-methyladenosine modification of the Aedes aegypti transcriptome and its alteration upon dengue virus infection in Aag2 cell line

Analysis of m(6)A RNA modifications in the mosquito transcriptome and their changes upon dengue virus infection provides insight into the role of epigenetics in regulating viral replication in mosquitoes. The N-6-methyladenosine (m(6)A) modification of RNA has been reported to affect viral infections. Studies have confirmed the role of m(6)A in replication of several vector-borne flaviviruses, including dengue virus (DENV), in mammalian cells. Here, we explored the role of m(6)A in DENV replication in the mosquito Aedes aegypti Aag2 cell line. We first determined the presence of m(6)A on the RNAs from mosquito cells and using methylated RNA immunoprecipitation and sequencing (MeRIP-Seq) identified m(6)A modification of the mosquito transcriptome and those that changed upon DENV infection. Depletion of m(6)A methyltransferases and the m(6)A binding protein YTHDF3 RNAs decreased the replication of DENV. In particular, we found that the Ae. aegypti ubiquitin carrier protein 9 (Ubc9) is m(6)A modified and its expression increases after DENV infection. Silencing of the gene and ectopic expression of Ubc9 led to reduced and increased DENV replication, respectively. The abundance of Ubc9 mRNA and its stability were reduced with the inhibition of m(6)A modification, implying that m(6)A modification of Ubc9 might enhance expression of the gene. We also show that the genome of DENV is m(6)A modified at five sites in mosquito cells. Altogether, this work reveals the involvement of m(6)A modification in Ae. aegypti-DENV interaction.