An RNA-centric dissection of host complexes controlling flavivirus infection [LAM-PCR]

Flaviviruses including dengue virus (DENV) and Zika virus (ZIKV) cause significant human disease. Co-opting cellular factors for viral protein translation and viral genome replication at the endoplasmic reticulum (ER) is a shared replication strategy, despite different clinical outcomes. While the protein products of these viruses have been studied in depth, how the RNA genomes operate inside human cells is poorly understood. Using comprehensive identification of RNA binding proteins by mass spectrometry (ChIRP-MS), we took an RNA-centric viewpoint of flaviviral infection and identified several hundred proteins associated with both DENV and ZIKV genomic RNA inside human cells. Intersection with genome-scale knockout screens assigned putative functional relevance to the RNA-protein interactions. ER RNA binding proteins such vigilin and RRBP1 directly bound viral RNA and each operated at distinct points in the life cycle of flaviviruses. Thus, this versatile strategy can elucidate features of human biology that control pathogenesis of clinically relevant viruses. This experiment was designed to assess, in a genome-wide manner, what human genes are required for the Zika virus to infect HAP1 cells. Genes were disrupted with lentiviral gene trap technology.