Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari , Bari , Italy ; Institute of Biomembranes and Bioenergetics , Bari , Italy.
RNA Editing Laboratory, Oncohaematology Department, IRCCS Ospedale Pediatrico Bambino Gesù , Rome , Italy.
Front Bioeng Biotechnol. 2014 Dec 5;2:64. doi: 10.3389/fbioe.2014.00064. eCollection 2014.
RNA editing is an important co/post-transcriptional molecular process able to modify RNAs by nucleotide insertions/deletions or substitutions. In human, the most common RNA editing event involves the deamination of adenosine (A) into inosine (I) through the adenosine deaminase acting on RNA proteins. Although A-to-I editing can occur in both coding and non-coding RNAs, recent findings, based on RNA-seq experiments, have clearly demonstrated that a large fraction of RNA editing events alter non-coding RNAs sequences including untranslated regions of mRNAs, introns, long non-coding RNAs (lncRNAs), and low molecular weight RNAs (tRNA, miRNAs, and others). An accurate detection of A-to-I events occurring in non-coding RNAs is of utmost importance to clarify yet unknown functional roles of RNA editing in the context of gene expression regulation and maintenance of cell homeostasis. In the last few years, massive transcriptome sequencing has been employed to identify putative RNA editing changes at genome scale. Despite several efforts, the computational prediction of A-to-I sites in complete eukaryotic genomes is yet a challenging task. We have recently developed a software package, called REDItools, in order to simplify the detection of RNA editing events from deep sequencing data. In the present work, we show the potential of our tools in recovering A-to-I candidates from RNA-Seq experiments as well as guidelines to improve the RNA editing detection in non-coding RNAs, with specific attention to the lncRNAs.
RNA 编辑是一种重要的转录后分子过程，能够通过核苷酸的插入/缺失或替换来修饰 RNA。在人类中，最常见的 RNA 编辑事件涉及通过作用于 RNA 的腺苷脱氨酶将腺苷 (A) 脱氨转化为肌苷 (I)。尽管 A 到 I 的编辑可以发生在编码和非编码 RNA 中，但基于 RNA-seq 实验的最近发现清楚地表明，很大一部分 RNA 编辑事件改变了非编码 RNA 序列，包括 mRNA 的非翻译区、内含子、长非编码 RNA (lncRNA) 和低分子量 RNA (tRNA、miRNA 等)。准确检测非编码 RNA 中发生的 A 到 I 事件对于阐明 RNA 编辑在基因表达调控和细胞内稳态维持中的未知功能作用至关重要。在过去的几年中，大规模转录组测序已被用于在全基因组范围内识别潜在的 RNA 编辑变化。尽管进行了多次尝试，但在完整的真核基因组中预测 A 到 I 位点仍然是一项具有挑战性的任务。我们最近开发了一个名为 REDItools 的软件包，用于简化从深度测序数据中检测 RNA 编辑事件。在本工作中，我们展示了我们的工具从 RNA-Seq 实验中恢复 A 到 I 候选者的潜力，以及改进非编码 RNA 中 RNA 编辑检测的指南，特别关注 lncRNA。
