Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, Virginia, USA.
Myles H. Thaler Center for AIDS and Human Retrovirus Research, University of Virginia, Charlottesville, Virginia, USA.
Wiley Interdiscip Rev RNA. 2021 Jan;12(1):e1631. doi: 10.1002/wrna.1631. Epub 2020 Oct 18.
Intron retention (IR) occurs when a complete and unspliced intron remains in mature mRNA. An increasing body of literature has demonstrated a major role for IR in numerous biological functions, including several that impact human health and disease. Although experimental technologies used to study other forms of mRNA splicing can also be used to investigate IR, a specialized downstream computational analysis is optimal for IR discovery and analysis. Here we provide a review of IR and its biological implications, as well as a practical guide for how to detect and analyze it. Several methods, including long read third generation direct RNA sequencing, are described. We have developed an R package, FakIR, to facilitate the execution of the bioinformatic tasks recommended in this review and a tutorial on how to fit them to users aims. Additionally, we provide guidelines and experimental protocols to validate IR discovery and to evaluate the potential impact of IR on gene expression and protein output. This article is categorized under: RNA Evolution and Genomics > Computational Analyses of RNA RNA Processing > Splicing Regulation/Alternative Splicing RNA Methods > RNA Analyses in vitro and In Silico.
内含子保留（IR）是指完整的、未经剪接的内含子保留在成熟的 mRNA 中。越来越多的文献表明，IR 在许多生物学功能中起着重要作用，包括一些影响人类健康和疾病的功能。虽然用于研究其他形式的 mRNA 剪接的实验技术也可用于研究 IR，但专门的下游计算分析是发现和分析 IR 的最佳方法。本文综述了 IR 及其生物学意义，以及检测和分析 IR 的实用指南。描述了包括第三代长读直接 RNA 测序在内的几种方法。我们开发了一个 R 包 FakIR，以方便执行本综述中推荐的生物信息学任务，并提供了一个教程，介绍如何将它们应用于用户目标。此外，我们还提供了验证 IR 发现的指南和实验方案，并评估了 IR 对基因表达和蛋白质输出的潜在影响。本文属于以下类别：RNA 进化和基因组学 > 计算分析 RNA RNA 加工 > 剪接调控/可变剪接 RNA 方法 > 体外和计算机分析 RNA。
