Discovery of Widespread Host Protein Interactions with the Pre-replicated Genome of CHIKV Using VIR-CLASP

The primary interactions between incoming viral RNA genomes and host proteins are crucial to infection and immunity. Until now, the ability to study these events was lacking. We developed viral cross-linking and solid-phase purification (VIR-CLASP) to characterize the earliest interactions between viral RNA and cellular proteins. We investigated the infection of human cells using Chikungunya virus (CHIKV) and influenza A virus and identified hundreds of direct RNA-protein interactions. Here, we explore the biological impact of three protein classes that bind CHIKV RNA within minutes of infection. We find CHIKV RNA binds and hijacks the lipid-modifying enzyme fatty acid synthase (FASN) for pro-viral activity. We show that CHIKV genomes are N6-methyladenosine modified, and YTHDF1 binds and suppresses CHIKV replication. Finally, we find that the innate immune DNA sensor IFI16 associates with CHIKV RNA, reducing viral replication and maturation. Our findings have direct applicability to the investigation of potentially all RNA viruses. [Display omitted] •VIR-CLASP identifies host protein interactions with incoming RNA viral genomes•VIR-CLASP can reveal the early interactomes of seven different viral families•The CHIKV genome binds to distinct proteins under different conditions and times•(Non)canonical RBPs like FASN, IFI16, and YTHDF1 uniquely regulate CHIKV replication The earliest interactions between incoming RNA viral genomes and host RNA-binding proteins can be crucial to viral replication. Until now, these events could not be distinctly studied. Kim et al. develop VIR-CLASP, demonstrate its extensibility across multiple viral families, and report their findings on the CHIKV and IAV interactomes.