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

TY - JOUR

T1 - miRNA-target chimeras reveal miRNA 3'-end pairing as a major determinant of Argonaute target specificity

AU - Moore, Michael J

AU - Scheel, Troels K H

AU - Luna, Joseph M

AU - Park, Christopher Y

AU - Fak, John J

AU - Nishiuchi, Eiko

AU - Rice, Charles M

AU - Darnell, Robert B

PY - 2015/11/25

Y1 - 2015/11/25

N2 - 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 1/4130,000 endogenous miRNA-target interactions in mouse brain and 1/440,000 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.

AB - 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 1/4130,000 endogenous miRNA-target interactions in mouse brain and 1/440,000 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.

U2 - 10.1038/ncomms9864

DO - 10.1038/ncomms9864

M3 - Journal article

C2 - 26602609

SN - 2041-1723

VL - 6

JO - Nature Communications

JF - Nature Communications

M1 - 8864

ER -