Detection of A-to-I microRNA editing with miRmedon reveals widespread co-editing of mature microRNA in the human brain

microRNA (miRNA), key regulators of gene expression, are prime targets for adenosine deaminase acting on RNA (ADAR) enzymes. Although ADAR-mediated adenosine-to-inosine (A-to-I) miRNA editing has been shown to be essential for orchestrating complex processes, including neurodevelopment and cancer progression, only few human miRNA editing sites have been reported. Several computational approaches have been developed for the detection of miRNA editing in small RNAseq data, all based on the identification of systematic mismatches of G at primary adenosine sites in known miRNA sequences. However, these methods have several limitations, including their ability to detect only one editing site per sequence (although editing of multiple sites per miRNA has been reproducibly validated), their focus on uniquely mapping reads (even though 20% of human miRNA are transcribed from multiple loci), and their inability to detect editing in miRNA harboring genomic variants (though 73% of human miRNA loci include a reported SNP or indel). To overcome these limitations, we developed miRmedon, that leverages large-scale human variation data, a combination of local and global alignments, and a comparison of the inferred editing and error distributions, for confident detection of miRNA editing in small RNAseq data. We demonstrate the improved performance of miRmedon as compared to currently available methods and describe its advantages. We further use miRmedon to discover editing haplotypes of mature human brain miRNA for the first time. We find that doubly edited mature miRNA are common in the adult human prefrontal cortex, most include a frequently edited site within the miRNA seed region, and are predicted to maintain a stable pre-miRNA structure. These results suggest that co-editing of mature miRNA could enable efficient shifting of gene expression programs.