Classification and Quantification of Unproductive Splicing Events

Abstract

In eukaryotic cells, the nonsense-mediated decay (NMD) pathway degrades mRNAs with premature stop codons. The coupling between NMD and alternative splicing (AS) generates NMD-sensitive transcripts (NMD targets, NMDTs) that play an important role in the gene expression regulation via the unproductive splicing mechanism. Understanding this mechanism requires proper identification of NMDT-generating AS events. Here, we developed NMDj, a tool for the identification, classification and quantification of NMDTgenerating AS events which does not rely on the best matching transcript partner principle employed by the existing methods. Instead, NMDj uses a set of characteristic introns that discriminate NMDTs from all protein-coding transcripts. The benchmark on simulated RNA-Seq data demonstrated that NMDj allows to quantify NMDT-generating AS events with better precision compared to other existing methods. NMDj represents a generic method suitable for the accurate classification of arbitrarily complex AS events that generate NMDTs. The NMDj pipeline is available through the repository https://github.com/zavilev/NMDj/.