TY - JOUR
T1 - Identification of RNA partners of viral proteins in infected cells
AU - Komarova, Anastassia V.
AU - Combredet, Chantal
AU - Sismeiro, Odile
AU - Dillies, Marie Agnès
AU - Jagla, Bernd
AU - David, Raul Yusef Sanchez
AU - Vabret, Nicolas
AU - Coppeé, Jean Yves
AU - Vidalain, Pierre Olivier
AU - Tangy, Fred́éric
N1 - Funding Information:
This work was supported by the Institut Pasteur and the CNRS. A.V.K was supported by a “Bourse Roux” (Institut Pasteur) and by the Agence Nationale de Recherches sur le SIDA et les Hépatites virales (ANRS).
PY - 2013/6
Y1 - 2013/6
N2 - 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.
AB - 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.
KW - Affinity purification
KW - Measles virus
KW - Next-generation sequencing
KW - Nucleocapsids
KW - RNA-protein interactions
KW - Tagged proteins
UR - http://www.scopus.com/inward/record.url?scp=84894582560&partnerID=8YFLogxK
U2 - 10.4161/rna.24453
DO - 10.4161/rna.24453
M3 - Article
C2 - 23595062
AN - SCOPUS:84894582560
SN - 1547-6286
VL - 10
SP - 943
EP - 956
JO - RNA Biology
JF - RNA Biology
IS - 6
ER -