Systematic analysis reveals cis and trans determinants affecting C-to-U RNA editing inArabidopsis thaliana
Systematic analysis reveals cis and trans determinants affecting C-to-U RNA editing inArabidopsis thaliana
复制标题
系统分析揭示影响拟南芥 C-to-U RNA 编辑的顺式和反式决定子
DOI：
10.1186/s12863-020-00907-6
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发表时间：
2020-09-03
期刊：
影响因子：
2.9
通讯作者：
Wei, Lai
中科院分区：
文献类型：
--
作者：
Chu, Duan;Wei, Lai
背景 C-to-U RNA 编辑在植物的线粒体和叶绿体基因中普遍存在。通过案例研究不断发现一小部分 C 到 U 编辑位点的生物学功能。然而，在全基因组水平上，影响这些C-to-U事件发生或编辑水平的顺式和反式决定簇的研究相对较少。已知的是，PPR（五肽重复）蛋白是负责 C 至 U 转化的主要反式调控元件，但其他决定因素，尤其是顺式调控元件在很大程度上仍未得到研究。结果通过分析拟南芥根和芽的转录组和翻译组数据，结合拟南芥和琴叶拟南芥杂交种的RNA-seq数据，我们对可能影响C-to-U编辑事件的顺式元件和反式调控元件进行了全基因组研究。上游鸟苷或双链 RNA (dsRNA) 区域不利于编辑事件。同时，包括转录因子在内的许多基因可能间接发挥反式调控作用。结论 5-素胸苷促进顺式编辑，而 dsRNA 结构阻止顺式编辑。许多转录因子影响反式编辑。尽管顺式和反式调控的详细分子机制仍有待实验验证，但我们的研究结果为研究植物 C 到 U RNA 编辑事件提供了新的视角。
Background C-to-U RNA editing is prevalent in the mitochondrial and chloroplast genes in plants. The biological functions of a fraction of C-to-U editing sites are continuously discovered by case studies. However, at genome-wide level, the cis and trans determinants affecting the occurrence or editing levels of these C-to-U events are relatively less studied. What is known is that the PPR (pentatricopeptide repeat) proteins are the main trans-regulatory elements responsible for the C-to-U conversion, but other determinants especially the cis-regulatory elements remain largely uninvestigated. Results By analyzing the transcriptome and translatome data inArabidopsis thalianaroots and shoots, combined with RNA-seq data from hybrids ofArabidopsis thalianaandArabidopsis lyrata, we perform genome-wide investigation on the cis elements and trans-regulatory elements that potentially affect C-to-U editing events. An upstream guanosine or double-stranded RNA (dsRNA) regions are unfavorable for editing events. Meanwhile, many genes including the transcription factors may indirectly play regulatory roles in trans. Conclusions The 5-prime thymidine facilitates editing and dsRNA structures prevent editing in cis. Many transcription factors affect editing in trans. Although the detailed molecular mechanisms underlying the cis and trans regulation remain to be experimentally verified, our findings provide novel aspects in studying the botanical C-to-U RNA editing events.