The study by Chi et al. (2009) utilized HITS-CLIP (crosslinking immunoprecipitation followed by high-throughput sequencing) to identify functional protein-RNA interaction sites in mouse brain. Specifically, they covalently crosslinked native Argonaute (Ago) protein-RNA complexes, generating two datasets: Ago-miRNA and Ago-mRNA binding sites. These datasets were combined with bioinformatic analysis to identify miRNA-target mRNA interaction sites. The authors validated genome-wide interaction maps for miR-124 and generated additional maps for the 20 most abundant miRNAs in P13 mouse brain. The Ago HITS-CLIP method provides a platform for exploring the specificity and range of miRNA action in vivo and identifies precise sequences for targeting clinically relevant miRNA-mRNA interactions. The study highlights the importance of direct protein-RNA interactions in miRNA regulation and demonstrates the utility of Ago HITS-CLIP in identifying functional miRNA targets.The study by Chi et al. (2009) utilized HITS-CLIP (crosslinking immunoprecipitation followed by high-throughput sequencing) to identify functional protein-RNA interaction sites in mouse brain. Specifically, they covalently crosslinked native Argonaute (Ago) protein-RNA complexes, generating two datasets: Ago-miRNA and Ago-mRNA binding sites. These datasets were combined with bioinformatic analysis to identify miRNA-target mRNA interaction sites. The authors validated genome-wide interaction maps for miR-124 and generated additional maps for the 20 most abundant miRNAs in P13 mouse brain. The Ago HITS-CLIP method provides a platform for exploring the specificity and range of miRNA action in vivo and identifies precise sequences for targeting clinically relevant miRNA-mRNA interactions. The study highlights the importance of direct protein-RNA interactions in miRNA regulation and demonstrates the utility of Ago HITS-CLIP in identifying functional miRNA targets.