Fig. 2: DNA methylation affects miRNA biogenesis.

a Mean methylated CpG signal plotted across 100 bp of miRNA region and an additional 200 bp of the flanking regions for top and bottom quartiles of miRNA expression. The miRNA region (100 bp) and 25 flanking bp between the two groups were tested for statistical significance. ***p < 0.0001; t-test. b Quantification of DNMT genomic presence by PCR for WT and TKO mouse ESCs. GAPDH was used as the loading control. Source data are provided as a Source Data file. c NanoString microarray miRNA expression data in WT vs. TKO cells. Representative miRNAs used for validation are highlighted with open black circles. d Plot of the mean differences in mature miRNA expression in WT vs. TKO mouse ESCs. miRNA expression was compared between WT and TKO cells within each group and for all the methylated groups together using one-sided paired t-test. p-values are given above each bar. e Efficiency values, calculated as the level of mature miRNA divided by the level of pri-miRNA for the methylated miRNAs and unmethylated miRNAs in WT and TKO mouse ESCs. Data were normalized to RPLP0 for pri-miRNAs and U6 for mature miRNAs. Error bars represent ± SEM (n = 3). * represents p < 0.05; ** represents p < 0.01; NS = Not Significant; t-test. Source data are provided as a Source Data file. f Plot of differential gene expression (log2 FPKM of WT/TKO) vs. differential mature miRNA expression as measured by NanoString analysis. R- and p-values of Pearson’s product-moment correlation are given.