Genetic methods for identification and characterization of RNA-RNA and RNA-protein interactions

Two general strategies using pseudorevertants have been useful in identifying RNA-RNA and RNA-protein interactions, direct synthesis of compensatory changes to test models or in vivo selection of suppressors. The most successful application of these approaches has been in the elucidation of RNA-RNA interactions, in a large part because the rules for RNA base pairing are, at least partially, understood. Beyond the initial identification of interactions, suppressors also provide important starting points for further analysis. In the case of an unknown gene product (i.e., the RNA16 gene product), the suppressor provides a route to cloning and analysis of the gene. In addition, the construction of a specific suppressor in a RNA molecule can provide a starting point for the dissection of the biogenesis and function of that RNA. This aspect is most important when the RNA in question normally provides an essential cellular role or is encoded by a multigene family. For example, the construction of a message-specific 16 S RNA in Escherichia coli should, in principle, allow for a genetic dissection of rRNA biogenesis and function.