Edited mature miRNAs alter miRNA targeting. (A) The editing site density in mature miRNAs. The significant difference between the seed region of the miRNA (bases 2–8; region 1) and the rest of the sites (bases 1 and 9–24; region 2) was calculated using χ2 test: (human) P = 1.0 × 10−12; (mouse) P = 6.5 × 10−6; (D.mel) P = 0.85. (B, top) For each miRNA that was edited in the seed region, we grouped its targets into three categories: targeted by unedited version only (loss), by both unedited and edited versions (common), and by edited version only (gain). (Bottom) The distribution of the number of “gain” group target genes shared by multiple neuronal edited miRNAs in human was shown as an example. (C) Functional enrichment for “gain” group genes targeted by neuronal or non-neuronal edited miRNAs in human. Human edited miRNAs identified in neuronal or non-neuronal tissues (Supplemental Table S7) were used for analysis. “Gain” group genes targeted by at least six neuronal or four non-neuronal edited miRNAs were used for analysis (Methods). The sets of transcripts coexpressed with the miRNAs were used as background. P-values were corrected for multiple hypotheses testing using the BH method. (D) Functional enrichment for “gain” group genes targeted by neuronal edited miRNAs in mouse. Mouse edited miRNAs identified in neuronal tissues (Supplemental Table S7) were used for analysis. “Gain” group genes targeted by at least six miRNAs (Methods) were used for analysis. The sets of transcripts coexpressed with the miRNAs were used as background. The P-values were corrected for multiple hypotheses testing using the BH method. The top 20 significant GO terms were shown. (E) The comparison of edited neuronal miRNA seeds between human and mouse. A conserved edited seed means that both the miRNA seed and the editing position are conserved in human and mouse.
