microRNA-seq of cartilage reveals an over-abundance of miR-140-3p which contains functional isomiRs

Woods, Steven, Charlton, Sarah, Cheung, Kathleen, Hao, Yao, Soul, Jamie, Reynard, Louise, Crowe, Natalie, Swingler, Tracey, Skelton, Andrew, Miles, Colin, Tsompani, Dimitra, Jackson, Robert, Dalmay, Tamas, Barter, Matt J., Clark, Ian and Young, David (2020) microRNA-seq of cartilage reveals an over-abundance of miR-140-3p which contains functional isomiRs. RNA. ISSN 1355-8382

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Abstract

MiR-140 is selectively expressed in cartilage. Deletion of the entire miR-140 locus in mice results in a growth retardation phenotype and an early-onset osteoarthritis-like pathology, however the relative contribution of miR-140-5p or miR-140-3p to the phenotype remains to be determined. An unbiased small RNA sequencing approach identified that miR-140-3p was in vast abundance (>10-fold) to miR-140-5p in human cartilage. Analysis of these data identified multiple miR-140-3p isomiRs differing from the miRBase [1] annotation at both the 5´ and 3´ end, with >99% of miR-140-3p isomiRs having one of two ‘seed’ sequences (5´ bases 2-8). The most abundant isomiR with each seed were selected for further analysis; miR-140-3p.2 which has an identical seed to the miRBase miR-140-3p (ACCACAG) and miR-140-3p.1 which has an altered seed (CCACAGG), and thus different potential targets. Each isomiR was overexpressed in chondrocytes and whole-genome transcriptomics used to identify targets. miR-140-3p.1 and miR-140-3p.2 significantly down-regulated 694 and 238 genes respectively (adj.P.Val<0.05), of which only 162 genes were commonly down-regulated by both isomiRs. Targets of both isomiRs were validated using 3´UTR luciferase assays. A significant enrichment of miR-140-3p.1 targets was identified within genes whose expression increase in the rib chondrocytes of Mir140-null mice and within genes whose expression decreased during human chondrogenesis. Finally, through imputing the expression of miR-140 from the expression of the host gene WWP2 in 124 previously published datasets an inverse correlation with miR-140-3p.1 predicted targets was identified. Together these data suggest the novel seed containing isomiR miR-140-3p.1 is more functional than the original consensus miR-140-3p or the isomiR with the same seed, miR-140-3p.2.

Item Type: Article
Faculty \ School: Faculty of Science > School of Biological Sciences
Depositing User: LivePure Connector
Date Deposited: 09 Jul 2020 00:08
Last Modified: 24 Sep 2020 00:02
URI: https://ueaeprints.uea.ac.uk/id/eprint/75976
DOI: 10.1261/rna.075176.120

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