Global analysis of AGO2-bound RNAs reveals that miRNAs induce cleavage of target RNAs with limited complementarity

• Published in: Biochimica et biophysica acta. Gene regulatory mechanisms 2017-11, Vol.1860 (11), p.1148-1158
• Main Authors: Jung, Eunsun, Seong, Youngmo, Jeon, Bohyun, Song, Hoseok, Kwon, Young-Soo
• Format: Article
• Language: English
• Subjects: AGO2 catalytic activity; Animals; Argonaute Proteins - metabolism; Base Pairing - physiology; Cells, Cultured; CrossLinking ImmunoPrecipitation; Gene Expression Regulation; HeLa Cells; HMGA2; Humans; Mice; Mice, SCID; MicroRNA; MicroRNAs - genetics; MicroRNAs - metabolism; Protein Binding; RNA Cleavage; RNA, Messenger - genetics; RNA, Messenger - metabolism
• ISSN: 1874-9399; 1876-4320
• DOI: 10.1016/j.bbagrm.2017.10.001

Among the four Argonaute family members in mammals, only AGO2 protein retains endonuclease activity and facilitates cleavage of target RNAs base-pairing with highly complementary guide RNAs. Despite the deeply conserved catalytic activity, only a small number of targets have been reported to extensively base pair with cognate miRNAs to be cleaved by AGO2. Here, we analyzed AGO2-bound RNAs by CrossLinking ImmunoPrecipitation (CLIP) of genetically modified cells that express epitope-tagged AGO2 from the native genomic locus. We found that HMGA2 mRNA is cleaved by AGO2 loaded with let-7 and miR-21. In contrast to the generally accepted notion, the base-pairing from the seed region to the cleavage site, rather than perfect or near perfect complementarity, was required for cleavage of the target mRNA in cells. Non-templated addition of nucleotides at the 3′ end of the cleaved RNA was observed, further supporting the AGO2-mediated cleavage. Based on the observation that the limited complementarity is the minimum requirement for cleavage, we found that AGO2-mediated cleavage of targets is more common than previously thought. Our result may explain the vital role of endonuclease activity in controlling miRNA-mediated gene regulation. •AGO2 can induce cleavage of targets by miRNAs with limited complementarity in cells.•AGO2-mediated cleavage is more prevalent than previously thought.•HMGA2, an oncogene in mesenchymal tumors, is cleaved by let-7 and miR-21.•The cleavage enhances the suppression of gene expression by miRNAs.