Extended Data Fig. 6: Deregulation of miR-140-5p-G targets in miR-140 mutant chondrocytes.
From: Gain-of-function mutation of microRNA-140 in human skeletal dysplasia
a, Cumulative distributions of fold changes of mRNAs with conserved and non-conserved 8mer target sites for miR-140-5p-WT, -5p-G, -3p.1, and -3p.2 between miR-140 mutant or null chondrocytes versus WT chondrocytes. P values (versus a control gene set) were calculated by one-sided Kolmogorov–Smirnov test for either direction: upregulation (U) or downregulation (D) with Bonferroni correction (control genes, n = 9,706; miR-140-5p-WT, n = 333; miR-140-5p-G, n = 608; miR-140-3p.1, n = 903; miR-140-3p.2, n = 603). b, Cumulative distributions of fold changes of mRNAs with all 8mer, 7mer-m8, 7mer-A1, and 6mer target sites for miR-140-5p-G (left) and miR-140-5p-WT (right) when comparing miR-140-G homozygous chondrocytes with WT chondrocytes. P values (versus a control gene set) were calculated by one-sided Kolmogorov–Smirnov test for either direction: upregulation (U) or downregulation (D) with Bonferroni correction. Left (miR-140-5p-G): no site, n = 7,684; 8mer, n = 608; 7mer-m8, n = 862; 7mer-A1, n = 1,741; 6mer, n = 2,497. Right (miR-140-5p-WT): no site, n = 7,453; 8mer, n = 333; 7mer-m8, n = 1,507; 7mer-A1, n = 710; 6mer, n = 3,093. c, Performance of TargetScan v7.0 for prediction of miR-140-5p-G targeting. Cumulative distribution plots (left) and box plots (right) of fold-change expression of predicted target gene sets grouped by CWCS. Expression levels of predicted target genes of miR-140-5p-G (top; no site, n = 7,684; top 128, n = 59; top 256, n = 129; top 512, n = 275; top 1,024, n = 559; top 2,048, n = 1178; all targets, n = 4,187) and miR-140-5p-WT (bottom; no site, n = 7,453; top 128, n = 68; top 256, n = 142; top 512, n = 311; top 1,024, n = 637; top 2,048, n = 1,235; all targets, n = 4,418) were analyzed. Gene expression of miR-140-G homozygous chondrocytes and WT chondrocytes was compared. All predictions were considered. High CWCS was associated with stronger target gene regulation for both miR-140-5p-G and miR-140-5p-WT, suggesting that miR-140-5p-G follows mechanisms of conventional miRNA targeting as well as other endogenous miRNAs. In box plots, center lines show medians; box limits indicate the 25th and 75th percentiles; whiskers extend to 1.5× the interquartile range. d, Box plots showing context++ scores for conserved (left) and all (right) predicted target sites for miR-140-5p-WT, -5p-G, -3p.1, and -3p.2. Consistent with the effects on target gene expression, miR-140-5p-WT and miR-140-5p-G show similar and higher predicted target site efficiency than miR-140-3p.1 and miR-140-3p.2. Center lines show medians; box limits indicate the 25th and 75th percentiles; whiskers extend to 1.5× the interquartile range. Left (conserved 8mer): miR-140-5p-WT, n = 96; miR-140-5p-G, n = 114; miR-140-3p.1, n = 222; miR-140-3p.2, n = 115. Right (conserved and non-conserved 8mer): miR-140-5p-WT, n = 524; miR-140-5p-G, n = 1,002; miR-140-3p.1, n = 1,405; miR-140-3p.2, n = 930.
