The chloroplast and mitochondrial C-to-U RNA editing in Arabidopsis thaliana shows signals of adaptation
The chloroplast and mitochondrial C-to-U RNA editing in Arabidopsis thaliana shows signals of adaptation
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DOI：
10.1002/pld3.169
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发表时间：
2019-09-01
期刊：
影响因子：
3
通讯作者：
Wei, Lai
中科院分区：
文献类型：
--
作者：
Chu, Duan;Wei, Lai
C-to-U RNA编辑是在RNA水平上将胞苷转化为尿苷的过程。在植物中，经历C-to-U RNA修饰的基因主要是叶绿体和线粒体基因。案例研究已经确定了C-to-U编辑在各种生物过程中的作用，但大多数C-to-U编辑事件的功能后果仍未被发现。我们检索了拟南芥根和芽的深度测序转录组数据，并分析了它们的C-to-U RNA编辑组和基因表达模式。我们调查了这些C-to-U编辑位点的编辑水平和保守模式。非同义C到U编辑事件的水平高于同义事件的水平。非同义编辑位点的比例高于中性预期。高度编辑的胞苷在DNA水平上更保守，并且基因表达水平与C-to-U编辑水平相关。我们的研究结果表明，全球C-to-U编辑组是由自然选择塑造的，许多非同义的C-to-U编辑事件是自适应的。编辑机制可能是积极的选择和保持，并可能对修饰的RNA产生深远的影响。
C-to-U RNA editing is the conversion from cytidine to uridine at RNA level. In plants, the genes undergo C-to-U RNA modification are mainly chloroplast and mitochondrial genes. Case studies have identified the roles of C-to-U editing in various biological processes, but the functional consequence of the majority of C-to-U editing events is still undiscovered. We retrieved the deep sequenced transcriptome data in roots and shoots of Arabidopsis thaliana and profiled their C-to-U RNA editomes and gene expression patterns. We investigated the editing level and conservation pattern of these C-to-U editing sites. The levels of nonsynonymous C-to-U editing events are higher than levels of synonymous events. The fraction of nonsynonymous editing sites is higher than neutral expectation. Highly edited cytidines are more conserved at DNA level, and the gene expression levels are correlated with C-to-U editing levels. Our results demonstrate that the global C-to-U editome is shaped by natural selection and that many nonsynonymous C-to-U editing events are adaptive. The editing mechanism might be positively selected and maintained and could have profound effects on the modified RNAs.