MiSiPi.Rna: an integrated tool for characterizing small regulatory RNA processing

Abstract

Argonaute proteins mediate gene silencing via small regulatory RNAs that are generated by distinctive biogenesis pathways. In animals, three main classes are recognized: ∼21–24 nucleotide (nt) microRNAs (miRNAs), ∼21–24 nt small-interfering RNAs (siRNAs), and ∼24–32 nt Piwi-interacting RNAs (piRNAs). Mechanistic understanding of these pathways was gained from genetic, biochemical, and genomic studies in a handful of model systems, where key ribonucleolytic events were identified that specify stereotyped positioning of small RNAs relative to their precursor transcripts. With burgeoning availability of assembled genomes and small RNA data, there are abundant opportunities to characterize the diversity of small RNAs across nonmodel organisms. While several tools are well-suited to analyze specific small RNA pathways, an integrated package that can help classify and interpret all three major classes of small RNAs is wanting. To address this need, we developed a simple and efficient R package (MiSiPi.Rna) that can generate a variety of plots and statistics for preselected loci, which enable the characterization of diverse biogenesis features of miRNAs, siRNAs, and piRNAs. MiSiPi.Rna requires minimal computational expertise to run and will facilitate efforts to annotate and analyze the major classes of Argonaute-based small regulatory RNAs in arbitrary species of choice.