Figure 2

Strategy for genome-wide target identification of miRNAs using RIP and gene expression profiling. HeLa cells are transfected either with miRNAs or control duplexes. From each transfection, total RNA as well as RISC-associated RNAs are isolated by Ago2 immunoprecipitation. All populations of RNAs are profiled by deep sequencing or in come cases, by microarray hybridization (see text). RNAs showing RISC-association in a miRNA dependent manner are identified by comparing the immunoprecipitated RNAs between the miRNA and control RNA transfection. mRNAs showing repression by the miRNAs are identified by comparing the total RNAs between the miRNA and control RNA transfection.