Intracellular detection of
virus infections is a critical component of innate immunity carried out by molecules known as pathogen recognition receptors (
PRRs). Activation of
PRRs by their respective
pathogen-associated molecular patterns (
PAMPs) leads to production of proinflamatory
cytokines, including type I IFN, and the establishment of an
antiviral state in the host. Out of all
PRRs found to date,
retinoic acid inducible gene I (RIG-I) has been shown to play a key role in recognition of RNA viruses. On the basis of in vitro and transfection studies, 5'ppp
RNA produced during virus replication is thought to bind and activate this important sensor. However, the nature of
RNA molecules that interact with endogenous RIG-I during the course of
viral infection has not been determined. In this work we use next-generation
RNA sequencing to show that RIG-I preferentially associates with shorter, 5'ppp containing
viral RNA molecules in infected cells. We found that during Sendai
infection RIG-I specifically bound the genome of the defective interfering (DI) particle and did not bind the full-length virus genome or any other viral RNAs. In
influenza-infected cells RIG-I preferentially associated with shorter genomic segments as well as subgenomic DI particles. Our analysis for the first time identifies RIG-I
PAMPs under natural
infection conditions and implies that full-length genomes of single segmented RNA virus families are not bound by RIG-I during
infection.