Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, P R China.
BMC Genomics. 2010 Dec 2;11 Suppl 4(Suppl 4):S12. doi: 10.1186/1471-2164-11-S4-S12.
RNA editing is a transcript-based layer of gene regulation. To date, no systemic study on RNA editing of plant nuclear genes has been reported. Here, a transcriptome-wide search for editing sites in nuclear transcripts of Arabidopsis (Arabidopsis thaliana) was performed.
MPSS (massively parallel signature sequencing) and PARE (parallel analysis of RNA ends) data retrieved from public databases were utilized, focusing on one-base-conversion editing. Besides cytidine (C)-to-uridine (U) editing in mitochondrial transcripts, many nuclear transcripts were found to be diversely edited. Interestingly, a sizable portion of these nuclear genes are involved in chloroplast- or mitochondrion-related functions, and many editing events are tissue-specific. Some editing sites, such as adenosine (A)-to-U editing loci, were found to be surrounded by peculiar elements. The editing events of some nuclear transcripts are highly enriched surrounding the borders between coding sequences (CDSs) and 3' untranslated regions (UTRs), suggesting site-specific editing. Furthermore, RNA editing is potentially implicated in new start or stop codon generation, and may affect alternative splicing of certain protein-coding transcripts. RNA editing in the precursor microRNAs (pre-miRNAs) of ath-miR854 family, resulting in secondary structure transformation, implies its potential role in microRNA (miRNA) maturation.
To our knowledge, the results provide the first global view of RNA editing in plant nuclear transcripts.
RNA 编辑是一种基于转录本的基因调控方式。迄今为止，尚未有关于植物核基因 RNA 编辑的系统研究报道。本文对拟南芥（Arabidopsis thaliana）核转录本中的编辑位点进行了全转录组搜索。
利用公共数据库中的 MPSS（大规模平行签名测序）和 PARE（RNA 末端平行分析）数据，重点研究了单碱基转换编辑。除了线粒体转录本中的胞嘧啶（C）到尿嘧啶（U）编辑外，还发现许多核转录本存在多样化的编辑。有趣的是，这些核基因中有相当一部分与叶绿体或线粒体相关功能有关，许多编辑事件具有组织特异性。一些编辑位点，如腺嘌呤（A）到 U 编辑位点，被发现周围有特殊的元件。一些核转录本的编辑事件在编码序列（CDS）和 3'非翻译区（UTR）边界周围高度富集，表明存在特定位置的编辑。此外，RNA 编辑可能涉及新的起始或终止密码子的产生，并可能影响某些蛋白编码转录本的可变剪接。ath-miR854 家族前体 microRNA（pre-miRNA）的 RNA 编辑导致二级结构转变，表明其在 miRNA 成熟过程中可能发挥作用。
据我们所知，这些结果提供了植物核转录本中 RNA 编辑的首个全局视图。
