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. By analyzing the transcriptome and translatome data in Arabidopsis thaliana roots and shoots, combined with RNA-seq data from hybrids of Arabidopsis thaliana and Arabidopsis 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. 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.

中文翻译：

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系统分析揭示了在拟南芥中影响C-U-U RNA编辑的顺式和反式决定簇。

C to U RNA编辑普遍存在于植物的线粒体和叶绿体基因中。通过案例研究不断发现一部分C-to-U编辑站点的生物学功能。但是，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。众所周知，PPR（五肽重复序列）蛋白是负责C到U转换的主要反式调节元件，但其他决定因素，尤其是顺式调节元件，目前仍未进行研究。通过分析拟南芥根和芽中的转录组和转录组数据，并结合拟南芥和拟南芥杂交种的RNA-seq数据，我们对可能影响C-to-U编辑事件的顺式和反式调控元件进行全基因组研究。上游鸟苷或双链RNA（dsRNA）区不利于编辑事件。同时，包括转录因子在内的许多基因可能间接地在反式中发挥调节作用。5-primy胸腺嘧啶核苷可促进编辑，dsRNA结构可防止顺式编辑。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，但我们的发现为研究植物C-to-U RNA编辑事件提供了新的方面。包括转录因子在内的许多基因可能在反式中间接发挥调节作用。5-primy胸腺嘧啶核苷可促进编辑，dsRNA结构可防止顺式编辑。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，但我们的发现为研究植物C-to-U RNA编辑事件提供了新的方面。包括转录因子在内的许多基因可能在反式中间接发挥调节作用。5-primy胸腺嘧啶核苷可促进编辑，dsRNA结构可防止顺式编辑。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，但我们的发现为研究植物C-to-U RNA编辑事件提供了新的方面。