miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades

TLDR

microRNAs are small non‑coding RNAs that regulate many animal genes and are involved in diverse biological processes, and although high‑throughput sequencing enables sensitive detection, accurately identifying miRNAs amid sequenced RNAs remains challenging. The authors developed miRDeep2, an improved algorithm to accurately identify canonical and non‑canonical miRNAs—including those from transposable elements—and to highlight high‑confidence candidates detected across multiple samples. miRDeep2 implements a computational pipeline that models miRNA biogenesis, validates accuracy by knocking down the pathway in human cells, and offers a lightweight expression‑profiling routine with low memory usage and interactive graphics. Across seven animal species, miRDeep2 achieved 98.6–99.9% accuracy, identified hundreds of novel miRNAs, and validation in human cells showed that most of the >100 novel miRNAs were specifically downregulated, confirming the predictions.

Abstract

microRNAs (miRNAs) are a large class of small non-coding RNAs which post-transcriptionally regulate the expression of a large fraction of all animal genes and are important in a wide range of biological processes. Recent advances in high-throughput sequencing allow miRNA detection at unprecedented sensitivity, but the computational task of accurately identifying the miRNAs in the background of sequenced RNAs remains challenging. For this purpose, we have designed miRDeep2, a substantially improved algorithm which identifies canonical and non-canonical miRNAs such as those derived from transposable elements and informs on high-confidence candidates that are detected in multiple independent samples. Analyzing data from seven animal species representing the major animal clades, miRDeep2 identified miRNAs with an accuracy of 98.6–99.9% and reported hundreds of novel miRNAs. To test the accuracy of miRDeep2, we knocked down the miRNA biogenesis pathway in a human cell line and sequenced small RNAs before and after. The vast majority of the >100 novel miRNAs expressed in this cell line were indeed specifically downregulated, validating most miRDeep2 predictions. Last, a new miRNA expression profiling routine, low time and memory usage and user-friendly interactive graphic output can make miRDeep2 useful to a wide range of researchers.