Zavileyskiy L G, Chernyavskaya E A, Vlasenok M A, Pervouchine D D
Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow, 121205 Russia.
Acta Naturae. 2025 Apr-Jun;17(2):75-85. doi: 10.32607/actanaturae.27572.
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/.
在真核细胞中，无义介导的衰变（NMD）途径会降解带有提前终止密码子的mRNA。NMD与可变剪接（AS）之间的偶联会产生对NMD敏感的转录本（NMD靶标，NMDTs），这些转录本通过无效剪接机制在基因表达调控中发挥重要作用。要理解这一机制，需要正确识别产生NMDT的AS事件。在此，我们开发了NMDj，这是一种用于识别、分类和量化产生NMDT的AS事件的工具，它不依赖于现有方法所采用的最佳匹配转录本伙伴原则。相反，NMDj使用一组特征性内含子，将NMDTs与所有蛋白质编码转录本区分开来。对模拟RNA测序数据的基准测试表明，与其他现有方法相比，NMDj能够更精确地量化产生NMDT的AS事件。NMDj是一种通用方法，适用于对产生NMDTs的任意复杂AS事件进行准确分类。可通过存储库https://github.com/zavilev/NMDj/获取NMDj流程。
