Detection of microRNA-target interactions by chimera PCR (ChimP)

Abstract

MicroRNAs (miRNAs) regulate gene expression by directing Argonaute proteins to target RNAs, which usually results in destabilization and translational inhibition of the target RNA. The prediction of animal miRNA target sites has remained a challenge due to the ability of miRNAs to bind target RNAs through imperfect base pairing. Recently, several labs have established methods to produce biochemical evidence of miRNA-target interactions by generating chimeric reads where the miRNA is ligated to its target RNA. Despite the insights that can be gained from chimera producing methods, the current approaches are inefficient, labor intensive and require computational expertise. Here we describe a method, called Chimera PCR (ChimP), for the validation or testing of specific miRNA-target interactions. This method allows for focused experiments to analyze miRNA targeting in a variety of conditions.