DRETools: A tool-suite for differential RNA editing detection

What is it about?

Recent tools to detect RNA editing have expanded our understanding of epitranscriptomics, linking changes in RNA editing to both disease and normal cellular processes. However, the research community currently lacks tools for determining if change in RNA editing or "differential editing" has occurred. To meet this need, we present DRETools, a command-line tool-set for finding differential editing among samples, editing islands, and editing sites.

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Why is it important?

RNA editing is a class of epitranscriptomic post-transcriptional modification found throughout metazoa consisting of the abundant conversion of adenosine-to-inosine (A-to-I) by ADARs (adenosine deaminases acting on RNA) and rare conversion of cytosine-to-uridine (C-to-U) by APOBEC (apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like). RNA editing is particularly interesting as it is detectable as A-to-G and C-to-T mismatches to the reference genome within standard RNA-sequencing data via specialized computational pipelines. An increasing number of studies link changes in editing at specific sites or clusters-of-sites to diseases, such as epilepsy and atherosclerosis. Yet, no software for detecting differential editing is available. To meet this need, we present DRETools: 1) to calculate units that help reduce sample-bias, similar to FPKM for RNA expression; and 2) to find differentially edited sites and editing islands (i.e., clusters of editing sites). Further, we showcase two examples of finding differential editing and related tasks with DREtools.

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