MiR-140 is selectively expressed in cartilage. Deletion of the entire miR-140 locus in mice results in growth retardation and 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 miR-140-3p as significantly more abundant (>10-fold) than miR-140-5p in human cartilage. Analysis of these data identified multiple miR-140-3p isomiRs differing from the miRBase annotation at both the 5 ' and 3 ' end, with >99% having one of two seed sequences (5 ' bases 2-8). Canonical (miR-140-3p.2) and shifted (miR-140-3p.1) seed isomiRs were overexpressed in chondrocytes and transcriptomics performed to identify targets. miR-140-3p.1 and miR-140-3p.2 significantly down-regulated 694 and 238 genes respectively, of which only 162 genes were commonly down-regulated. IsomiR targets were validated using 3 'UTR luciferase assays. miR-140-3p.1 targets were enriched within up-regulated genes in rib chondrocytes of Mir140-null mice and within down-regulated genes 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 original consensus miR-140-3p seed containing isomiR.
MATERIAL AND METHODS
Analysis of cartilage sRNA-seqsRNA-seq was analysed as previously described (10). 5' isomiRs were defined using the following criteria: 1) loss or gain of 1 or more nucleotides, using the mature miRBase (11) sequences as a reference; 2) a read count >100, and 3) a read count > 5% of the mature miRBase reference sequence for that miRNA.
Human articular chondrocyte isolation, culture and transfectionHuman articular chondrocyte isolation from knee cartilage was performed as previously described (9). Tissue was donated by patients with diagnosed osteoarthritis and undergoing joint replacement surgery, with informed consent and ethics committee approval. Briefly, macroscopically normal cartilage was removed from the subchondral bone and dissected into ~1mm pieces using scalpel and forceps. Enzymatic digestion was performed using trypsin and then collagenase overnight at 37 o C. Chondrocytes were then grown to confluence and plated into 6 well plates for miRNA/isomiR mimic transfection. 100nM miRNA mimic and control were transfected into HAC using DharmaFECT 1 transfection reagent (Dharmacon, Horizon Discovery, Cambridge, UK) according to the manufacturer's protocol and essentially as previously described (9). 48h post-transfection HAC were lysed and RNA harvested using Qiagen miRNeasy kit (Qiagen, Crawley, UK). Custom miRNA mimics with each isomiR sequence were purchased from Dharmacon.