Isolation of RIG-I-associated RNAs from virus-infected cells

When a novel innate pattern recognition receptor (PRR) is identified, a question comes up immediately: Which molecular pattern(s) can it recognize? One approach that can be taken to answer this question for nucleic acid-binding receptors is the detailed analysis of synthetic ligands (DNA, RNA, or hybrids) to narrow in on the minimal patterns that activate a given receptor. However, this may not always lead to a satisfying answer. A complementary albeit technically more demanding way to tackle this question is to examine which nucleic acids are actually bound by the receptor in a setting of cellular infection. Here, we describe a basic protocol to isolate RNAs bound to the RNA receptors of the RIG-I-like helicase family from virus-infected cells via immunoprecipitation (IP). The isolated RNA can then be used to analyze its origin, characteristics, and immunostimulatory properties with a variety of methods.