Detecting agotrons in Ago CLIPseq data

Abstract

Timely and accurate regulation of gene expression is essential to all organisms. MicroRNAs (miRNAs) are a well-characterized and important class of gene expression regulators. We recently identified a novel class of gene regulators, the agotrons. Agotrons derive from short introns and associate with Argonaute (Ago) proteins much similar to miRNAs. However, agotrons completely bypass the conventional miRNA biogenesis pathway and thus exist as full-length introns, which disobey the classical rules on Ago-substrate requirements. As a class, agotrons are conserved in mammals, and despite the non-canonical biogenesis pathway, agotrons maintain the ability to deregulate mRNAs with seed-matches in the 3′UTR. While several pipelines exist for the detection of miRNAs, no bioinformatics toolkit has yet been developed to specifically identify agotrons. Here, we describe a simple approach, termed agotron_detector (https://github.com/ncrnalab/agotron_detector), to identify and quantify agotrons in Ago CLIPseq datasets. Hopefully, this allows researchers worldwide to characterize agotrons in more detail and to reveal the biological relevance of these fascinating RNA species.