Effect of genetic deletion of DROSHA on mature miRNA expression. (A) Plot of global differential miRNA expression from RNA-seq of DROSHA−/− relative to WT HCT116 cells with miRNAs from miRBase with read cutoff at one transcript per million (TPM) for displayed miRNAs (N = 3). (B) Plot of global differential miRNA expression from RNA-seq of DROSHA−/− relative to WT HCT116 cells with miRNAs from MirGeneDB with read cutoff at 1 TPM for displayed miRNAs. (C) Volcano plot where gray dots represent miRNAs that were reported as DROSHA-independent, and pink dots represent miRNAs that were reported as DROSHA-dependent. Differential expression and significance (adjusted P-value) calculated with edgeR, and dotted lines represent two log2 fold-changes. (D) Volcano plot showing differential expression and significance of miRNAs that are listed in MirGeneDB in DROSHA−/− cells relative to WT HCT116. (E) Volcano plot of differential expression in DROSHA−/− relative to WT cells from small-RNA-seq showing only the top 100 miRNAs associated with AGO2 from AGO2-eCLIP in WT HCT116 cells. (F) Venn diagram showing overlap between miRNAs highly associated with AGO2 (top 100 AGO2-eCLIP) and miRNAs that were reported DROSHA-dependent in biochemical assays.
