Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps

Nature. 2009 Jul 23;460(7254):479-86. doi: 10.1038/nature08170. Epub 2009 Jun 17.


MicroRNAs (miRNAs) have critical roles in the regulation of gene expression; however, as miRNA activity requires base pairing with only 6-8 nucleotides of messenger RNA, predicting target mRNAs is a major challenge. Recently, high-throughput sequencing of RNAs isolated by crosslinking immunoprecipitation (HITS-CLIP) has identified functional protein-RNA interaction sites. Here we use HITS-CLIP to covalently crosslink native argonaute (Ago, also called Eif2c) protein-RNA complexes in mouse brain. This produced two simultaneous data sets-Ago-miRNA and Ago-mRNA binding sites-that were combined with bioinformatic analysis to identify interaction sites between miRNA and target mRNA. We validated genome-wide interaction maps for miR-124, and generated additional maps for the 20 most abundant miRNAs present in P13 mouse brain. Ago HITS-CLIP provides a general platform for exploring the specificity and range of miRNA action in vivo, and identifies precise sequences for targeting clinically relevant miRNA-mRNA interactions.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Cross-Linking Reagents / chemistry
  • Cross-Linking Reagents / metabolism
  • Gene Expression Regulation*
  • HeLa Cells
  • Humans
  • Immunoprecipitation / methods*
  • Mice
  • MicroRNAs / metabolism*
  • Protein Interaction Mapping
  • Reproducibility of Results


  • Cross-Linking Reagents
  • MIRN124 microRNA, human
  • MicroRNAs
  • Mirn124 microRNA, mouse

Associated data

  • GEO/GSE16338