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

Byungil Kim, Sarah Arcos, Katherine Rothamel, Jeffrey Jian, Kristie L. Rose, W. Hayes McDonald, Yuqi Bian, Seth Reasoner, Nicholas J. Barrows, Shelton Bradrick, Mariano A. Garcia-Blanco, Manuel Ascano

Research output: Contribution to journalArticlepeer-review

14 Scopus citations


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.

Original languageEnglish (US)
Pages (from-to)624-640.e7
JournalMolecular cell
Issue number4
StatePublished - May 21 2020
Externally publishedYes


  • RNA virus
  • RNA-binding protein
  • host-pathogen interactions
  • innate immunity
  • interactome capture

ASJC Scopus subject areas

  • Molecular Biology
  • Cell Biology


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