Identification of RNA partners of viral proteins in infected cells

Anastassia V. Komarova, Chantal Combredet, Odile Sismeiro, Marie Agnès Dillies, Bernd Jagla, Raul Yusef Sanchez David, Nicolas Vabret, Jean Yves Coppeé, Pierre Olivier Vidalain, Fred́éric Tangy

Research output: Contribution to journalArticlepeer-review

17 Scopus citations

Abstract

RNA viruses exhibit small-sized genomes encoding few proteins, but still establish complex networks of protein-protein and RNA-protein interactions within a cell to achieve efficient replication and spreading. Deciphering these interactions is essential to reach a comprehensive understanding of the viral infection process. To study RNA-protein complexes directly in infected cells, we developed a new approach based on recombinant viruses expressing tagged viral proteins that were purified together with their specific RNA partners. High-throughput sequencing was then used to identify these RNA molecules. As a proof of principle, this method was applied to measles virus nucleoprotein (MV-N). It revealed that in addition to full-length genomes, MV-N specifically interacted with a unique population of 5′ copy-back defective interfering RNA genomes that we characterized. Such RNA molecules were able to induce strong activation of interferon-stimulated response element promoter preferentially via the cytoplasmic pattern recognition receptor RIG-I protein, demonstrating their biological functionality. Thus, this method provides a new platform to explore biologically active RNA-protein networks that viruses establish within infected cells.

Original languageEnglish
Pages (from-to)943-956
Number of pages14
JournalRNA Biology
Volume10
Issue number6
DOIs
StatePublished - Jun 2013
Externally publishedYes

Keywords

  • Affinity purification
  • Measles virus
  • Next-generation sequencing
  • Nucleocapsids
  • RNA-protein interactions
  • Tagged proteins

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