Ago HITS-CLIP decodes miRNA-mRNA interaction maps

MicroRNAs (miRNAs) play critical roles in the regulation of gene expression. However, since miRNA activity requires base pairing with only 6-8 nucleotides of mRNA, predicting target mRNAs is a major challenge. Recently, high-throughput sequencing of RNAs isolated by crosslinking immunoprecipitation...

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Bibliographic Details
Published inNature (London) Vol. 460; no. 7254; pp. 479 - 486
Main Authors Chi, Sung Wook, Zang, Julie B., Mele, Aldo, Darnell, Robert B.
Format Journal Article
LanguageEnglish
Published 17.06.2009
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Summary:MicroRNAs (miRNAs) play critical roles in the regulation of gene expression. However, since miRNA activity requires base pairing with only 6-8 nucleotides of mRNA, 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) protein-RNA complexes in mouse brain. This produced two simultaneous datasets—Ago-miRNA and Ago-mRNA binding sites—that were combined with bioinformatic analysis to identify miRNA-target mRNA interaction sites. 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.
Bibliography:Author Contributions S.W.C. and R.B.D conceived, designed and supervised the experiments, analyzed the data and wrote the paper. J.B.Z did the initial experiments with the 7G1-1* antibody. A.M. helped with all HITS-CLIP experiments.
ISSN:0028-0836
1476-4687
DOI:10.1038/nature08170