High-Resolution In Vivo Identification of miRNA Targets by Halo-Enhanced Ago2 Pull-Down

The identification of microRNA (miRNA) targets by Ago2 crosslinking-immunoprecipitation (CLIP) methods has provided major insights into the biology of this important class of non-coding RNAs. However, these methods are technically challenging and not easily applicable to an in vivo setting. To overcome these limitations and facilitate the investigation of miRNA functions in vivo, we have developed a method based on a genetically engineered mouse harboring a conditional Halo-Ago2 allele expressed from the endogenous Ago2 locus. By using a resin conjugated to the HaloTag ligand, Ago2-miRNA-mRNA complexes can be purified from cells and tissues expressing the endogenous Halo-Ago2 allele. We demonstrate the reproducibility and sensitivity of this method in mouse embryonic stem cells, developing embryos, adult tissues, and autochthonous mouse models of human brain and lung cancers. This method and the datasets we have generated will facilitate the characterization of miRNA-mRNA networks in vivo under physiological and pathological conditions. [Display omitted] •The authors describe a mouse strain harboring a Cre-regulated Halo-Ago2 knockin allele•The model streamlines the experimental identification of miRNA-mRNA interactions•The authors identify miRNA targets in mESCs, embryos, normal tissues, and tumors Li, Pritykin, Concepcion et al. report the development of Halo-enhanced Ago2 pull-down (HEAP), a method that streamlines the experimental identification of Ago2-miRNA-mRNA interaction sites in murine cells and tissues.