Article open access publication

miRNA–target chimeras reveal miRNA 3′-end pairing as a major determinant of Argonaute target specificity

Nature Communications, Springer Nature, ISSN 2041-1723

Volume 6, 1, 2015

DOI:10.1038/ncomms9864, Dimensions: pub.1031013262, PMC: PMC4674787, PMID: 26602609,


Scheel, Troels K. H. (1) (2) (3)
Darnell, Robert B * (1) (4)

* Corresponding author



  1. (1) Rockefeller University, grid.134907.8
  2. (2) Department of Infectious Diseases and Clinical Research Centre, Copenhagen Hepatitis C Program (CO-HEP), Copenhagen University Hospital, 2650Hvidovre, Denmark
  3. (3) University of Copenhagen, grid.5254.6, KU
  4. (4) New York Genome Center, grid.429884.b


microRNAs (miRNAs) act as sequence-specific guides for Argonaute (AGO) proteins, which mediate posttranscriptional silencing of target messenger RNAs. Despite their importance in many biological processes, rules governing AGO-miRNA targeting are only partially understood. Here we report a modified AGO HITS-CLIP strategy termed CLEAR (covalent ligation of endogenous Argonaute-bound RNAs)-CLIP, which enriches miRNAs ligated to their endogenous mRNA targets. CLEAR-CLIP mapped ∼130,000 endogenous miRNA-target interactions in mouse brain and ∼40,000 in human hepatoma cells. Motif and structural analysis define expanded pairing rules for over 200 mammalian miRNAs. Most interactions combine seed-based pairing with distinct, miRNA-specific patterns of auxiliary pairing. At some regulatory sites, this specificity confers distinct silencing functions to miRNA family members with shared seed sequences but divergent 3'-ends. This work provides a means for explicit biochemical identification of miRNA sites in vivo, leading to the discovery that miRNA 3'-end pairing is a general determinant of AGO binding specificity.


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