State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China.
Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, USA.
Methods Mol Biol. 2021;2181:35-50. doi: 10.1007/978-1-0716-0787-9_3.
RNA editing is an important posttranscriptional process that alters the genetic information of RNA encoded by genomic DNA. Adenosine-to-inosine (A-to-I) editing is the most prevalent type of RNA editing in animal kingdom, catalyzed by adenosine deaminases acting on RNA (ADARs). Recently, genome-wide A-to-I RNA editing is discovered in fungi, involving adenosine deamination mechanisms distinct from animals. Aiming to draw more attention to RNA editing in fungi, here we discuss the considerations for deep sequencing data preparation and the available various methods for detecting RNA editing, with a special emphasis on their usability for fungal RNA editing detection. We describe computational protocols for the identification of candidate RNA editing sites in fungi by using two software packages REDItools and RES-Scanner with RNA sequencing (RNA-Seq) and genomic DNA sequencing (DNA-Seq) data.
RNA 编辑是一种重要的转录后过程，它改变了基因组 DNA 编码的 RNA 的遗传信息。腺苷到肌苷（A-to-I）编辑是动物界最普遍的 RNA 编辑类型，由作用于 RNA 的腺苷脱氨酶（ADARs）催化。最近，在真菌中发现了全基因组 A-to-I RNA 编辑，涉及与动物不同的腺苷脱氨机制。为了引起人们对真菌中 RNA 编辑的更多关注，在这里我们讨论了用于深度测序数据准备的注意事项以及用于检测 RNA 编辑的各种可用方法，特别强调了它们在真菌 RNA 编辑检测中的可用性。我们描述了使用两个软件包 REDItools 和 RES-Scanner 通过 RNA 测序（RNA-Seq）和基因组 DNA 测序（DNA-Seq）数据鉴定真菌中候选 RNA 编辑位点的计算方案。
