MiR-CLIP reveals iso-miR selective regulation in the miR-124 targetome. Issue 1 (9th December 2020)

• Record Type: Journal Article
• Authors: Wang, Yuluan; Soneson, Charlotte; Malinowska, Anna L; Laski, Artur; Ghosh, Souvik; Kanitz, Alexander; Gebert, Luca F R; Robinson, Mark D; Hall, Jonathan
• Is Part Of: Nucleic acids research. Volume 49:Issue 1(2021)
• Page Start: 25
• Page End: 37
• Publication Date: 2020-12-09
• Subjects: Nucleic acids -- Periodicals; Molecular biology -- Periodicals; 572.805
• DOI: 10.1093/nar/gkaa1117
• Languages: English
• ISSNs: 0305-1048

Abstract

Abstract: Many microRNAs regulate gene expression via atypical mechanisms, which are difficult to discern using native cross-linking methods. To ascertain the scope of non-canonical miRNA targeting, methods are needed that identify all targets of a given miRNA. We designed a new class of miR-CLIP probe, whereby psoralen is conjugated to the 3p arm of a pre-microRNA to capture targetomes of miR-124 and miR-132 in HEK293T cells. Processing of pre-miR-124 yields miR-124 and a 5′-extended isoform, iso -miR-124. Using miR-CLIP, we identified overlapping targetomes from both isoforms. From a set of 16 targets, 13 were differently inhibited at mRNA/protein levels by the isoforms. Moreover, delivery of pre-miR-124 into cells repressed these targets more strongly than individual treatments with miR-124 and iso -miR-124, suggesting that isomirs from one pre-miRNA may function synergistically. By mining the miR-CLIP targetome, we identified nine G-bulged target-sites that are regulated at the protein level by miR-124 but not isomiR-124. Using structural data, we propose a model involving AGO2 helix-7 that suggests why only miR-124 can engage these sites. In summary, access to the miR-124 targetome via miR-CLIP revealed for the first time how heterogeneous processing of miRNAs combined with non-canonical targeting mechanisms expand the regulatory range of a miRNA.