Sep 19, 2019

miRmedon: confident detection of microRNA editing

BioRxiv : the Preprint Server for Biology
Amitai Mordechai, Alal Eran

Abstract

microRNA (miRNA), key regulators of gene expression, are prime targets for adenosine deaminase acting on RNA (ADAR) enzymes. Although ADAR-mediated A-to-I miRNA editing has been shown to be essential for orchestrating complex processes, including neurodevelopment and cancer progression, only a 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 (although 20% of human miRNA are transcribed from multiple loci), and their inability to detect editing in miRNA genes harboring genomic variants (although 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 a confid...Continue Reading

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Mentioned in this Paper

ADAR
MicroRNA Gene
Adenosine
Sequence Determinations, RNA
Cancer Progression
Gene Expression
Site
Local
Adenosine Deaminase
Single Nucleotide Polymorphism

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