State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK; College of Life Sciences, University of Chinese Academy of Sciences, 100049, Beijing, China; CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK.
Department of Computational and Systems Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK.
Mol Plant. 2018 Apr 2;11(4):607-622. doi: 10.1016/j.molp.2018.01.008. Epub 2018 Feb 1.
RNA secondary structure plays a critical role in gene regulation. Rice (Oryza sativa) is one of the most important food crops in the world. However, RNA structure in rice has scarcely been studied. Here, we have successfully generated in vivo Structure-seq libraries in rice. We found that the structural flexibility of mRNAs might associate with the dynamics of biological function. Higher N-methyladenosine (mA) modification tends to have less RNA structure in 3' UTR, whereas GC content does not significantly affect in vivo mRNA structure to maintain efficient biological processes such as translation. Comparative analysis of RNA structurome between rice and Arabidopsis revealed that higher GC content does not lead to stronger structure and less RNA structural flexibility. Moreover, we found a weak correlation between sequence and structure conservation of the orthologs between rice and Arabidopsis. The conservation and divergence of both sequence and in vivo RNA structure corresponds to diverse and specific biological processes. Our results indicate that RNA secondary structure might offer a separate layer of selection to the sequence between monocot and dicot. Therefore, our study implies that RNA structure evolves differently in various biological processes to maintain robustness in development and adaptational flexibility during angiosperm evolution.
RNA 二级结构在基因调控中起着至关重要的作用。水稻（Oryza sativa）是世界上最重要的粮食作物之一。然而，水稻中的 RNA 结构却很少被研究。在这里，我们成功地在水稻中生成了体内结构测序文库。我们发现，mRNA 的结构灵活性可能与生物功能的动态有关。较高的 N6-甲基腺苷（m6A）修饰往往在 3'UTR 中具有较少的 RNA 结构，而 GC 含量不会显著影响体内 mRNA 结构，以维持高效的生物过程，如翻译。水稻和拟南芥之间的 RNA 结构组比较分析表明，较高的 GC 含量不会导致更强的结构和更少的 RNA 结构灵活性。此外，我们发现水稻和拟南芥之间的直系同源物的序列和结构保守性之间存在弱相关性。序列和体内 RNA 结构的保守性和分歧对应于不同的和特定的生物过程。我们的研究结果表明，RNA 二级结构可能为单子叶植物和双子叶植物之间的序列提供了一个独立的选择层。因此，我们的研究表明，RNA 结构在不同的生物过程中进化方式不同，以在被子植物进化过程中保持发育的稳健性和适应灵活性。
