ZIKV and DENV-2 sfRNA RNA Pull down Hela extract LC-MSMS

Insect-borne flaviviruses produce a 300-500 base long noncoding RNA, termed sfRNA, by stalling the cellular 5’-3’ exoribonuclease XRN1 via structures located in their 3’ untranslated regions. In this study we demonstrate that the production of sfRNAs by Zika virus results in the repression of XRN1 similar to what we have previously shown for other flaviviruses. Using protein-RNA reconstitution and a stringent RNA pulldown assay, we demonstrate that the sfRNA from both dengue type 2 and Zika viruses interact with a common set of 21 RNA binding proteins that influence post-transcriptional processes in the cell, including splicing, RNA stability and translation. We demonstrate that four of these interacting proteins - DDX6 and EDC3 (RNA decay factors), PHAX1 (a regulator of the biogenesis of the splicing machinery) and APOBEC3C (a nucleic acid editing deaminase) are inherently antiviral restriction factors for Zika virus infection. Furthermore, we demonstrate that cellular mRNA decay regulation as well as cellular RNA splicing are compromised during Zika virus infection. Collectively, these data demonstrate the large extent in which Zika virus sfRNAs interact with cellular RNA binding proteins as well as the potential for widespread dysregulation of post-transcriptional control which likely limits the effective response of the cell to viral infection.