Extended Data Fig. 7: Transcriptome-wide analysis of 7o8G-miR-1-delivered mouse hearts.
From: Position-specific oxidation of miR-1 encodes cardiac hypertrophy
a, Kolmogorov–Smirnov test results for Fig. 5a. There are significant downregulation (P = 5.4 × 10−23) of mRNAs with 7oxo site (6mer, positions 2–7, in 3′UTR) and significant upregulation (P = 1.6 × 10−35) of mRNAs with no site (neither miR-1 7oxo site nor seed site, 6mers) depending on 7o8G-miR-1 expression, relative to total (total mRNAs). But, mRNA with control site (“cont site”, mismatched site at position 6 of miR-1 in 3′UTRs but no 7oxo site in the transcript, previously reported to be unrecognized by miRNA32) showed no significance. b, CDF analysis for mRNAs with miR-1 7oxo site (7mer, position 2-8, in 3′UTR, n = 952, red line) depending on 7o8G-miR-1-mediated fold change (log2 ratio, x-axis), conducted for each replicate pairs (Exp A, B and C; Supplementary Table 2a) and also for combined results (Exp(A+B+C)). c, Kolmogorov–Smirnov test results for b, relative to total. d, Functional annotation results for downregulated DEG with miR-1 7oxo site in Fig. 5b, performed by DAVID (https://david.ncifcrf.gov) using BIOCARTA and KEGG pathways (top left). The most significantly enriched pathway, “skeletal mouse hypertrophy regulated via AKT/mTOR pathway” (P = 0.02) in BIOCARTA were indicated with other components of hits in the table (red; bottom left) and pathway map (red star; right). GSK3B is highlighted with red dotted circle. Notably, activation of GSK3B has been reported to suppress cardiac hypertrophy25. e–g, Concentrating on heart-related pathways in the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, the normalized enrichment score (NES) from gene set enrichment analysis (GSEA) elucidated “hypertrophic cardiomyopathy” (HCM, NES = 1.25; e, right), “arrhythmogenic right ventricular cardiomyopathy” (ARVC, NES = 1.20; f, right), and “dilated cardiomyopathy” (DCM, NES = 1.25; g, top) as pathways regulated by 7o8G-miR-1. Heat maps on the top indicate the mRNAs in the corresponding pathway with measured expression; red, downregulation; blue, upregulation; order of results from top, NT (n = 3), 7o8G-miR-1 (n = 3). Hits from downregulated DEG with miR-1 7oxo site in Fig. 5b were also displayed as red stars in HCM (e, left), ARVC (f, left) and DCM (only a distinct part from HCM and ARVC is displayed; g, bottom). ATP2A2 (SERCA2) is highlighted with red dotted circle and GJA1 (CX43) with blue dotted circle.
