Unraveling the role of tRNA-derived fragments in dengue virus pathogenesis: RNA-seq analysis and functional characterization

Dengue virus (DENV), a mosquito-borne virus of the Flaviviridae family, is a major cause of global morbidity and mortality. In our previous study, we performed RNA sequencing analysis, which showed that DENV infection increases tRNA fragmentation, leading to the generation of tRNA-derived small RNAs (tsRNAs). From RNA sequencing analysis, we identified differentially expressed tsRNAs, predominantly comprising of tRNA-derived fragments (tRFs), a class of tsRNAs. In this study, we have performed orthogonal validation of highly differentially expressed tRFs using northern blotting and have further investigated the functional role of these tRFs during DENV infection. Antisense oligos (ASOs) were used to inhibit the selected tRFs, and the effect of tRF inhibition on DENV replication was observed. Our results show that tRFs exhibit dual regulatory roles by either promoting or inhibiting the DENV replication through modulation of the PI3K pathway. Overall, this study identifies novel regulatory roles for tsRNAs in DENV pathogenesis and provides new insights into host–virus interactions.