Elucidating the editome: bioinformatics approaches for RNA editing detection
Elucidating the editome: bioinformatics approaches for RNA editing detection
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DOI：
10.1093/bib/bbx129
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发表时间：
2019-03-01
影响因子：
9.5
通讯作者：
Picardi, Ernesto
中科院分区：
文献类型：
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作者：
Diroma, Maria Angela;Ciaccia, Loredana;Picardi, Ernesto
RNA编辑是一种广泛存在的通过特异性核苷酸修饰影响初级RNA的共/转录后机制，在包括基因表达调控和/或非编码RNA加工在内的分子过程中发挥着相关作用。近年来，通过高通量RNA测序（RNA- seq）技术的可用性，编辑位点的检测得到了改进。准确的生物信息学管道对于下一代测序（NGS）数据分析至关重要，以确保正确识别编辑位点。使用各种读取映射器和具有广泛可调参数的变体调用器的几个管道可用于检测RNA编辑事件。在这篇综述中，我们讨论了一些最新和流行的工具，并为RNA- seq数据的生成和分析提供指导，以检测大量转录组数据中的RNA编辑。通过模拟和真实的数据集，我们概述了它们的行为，强调在NGS数据集中进行RNA编辑检测仍然是一项具有挑战性的任务。
RNA editing is a widespread co/posttranscriptional mechanism affecting primary RNAs by specific nucleotide modifications, which plays relevant roles in molecular processes including regulation of gene expression and/or the processing of noncoding RNAs. In recent years, the detection of editing sites has been improved through the availability of high-throughput RNA sequencing (RNA-Seq) technologies. Accurate bioinformatics pipelines are essential for the analysis of next-generation sequencing (NGS) data to ensure the correct identification of edited sites. Several pipelines, using various read mappers and variant callers with a wide range of adjustable parameters, are available for the detection of RNA editing events. In this review, we discuss some of the most recent and popular tools and provide guidelines for RNA-Seq data generation and analysis for the detection of RNA editing in massive transcriptome data. Using simulated and real data sets, we provide an overview of their behavior, emphasizing the fact that the RNA editing detection in NGS data sets remains a challenging task.