Rice In Vivo RNA Structurome Reveals RNA Secondary Structure Conservation and Divergence in Plants.
Rice In Vivo RNA Structurome Reveals RNA Secondary Structure Conservation and Divergence in Plants.
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DOI：
10.1016/j.molp.2018.01.008
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发表时间：
2018-04-02
期刊：
影响因子：
27.5
通讯作者：
Ding Y
中科院分区：
文献类型：
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作者：
Deng H;Cheema J;Zhang H;Woolfenden H;Norris M;Liu Z;Liu Q;Yang X;Yang M;Deng X;Cao X;Ding Y
RNA二级结构在基因调控中起着关键作用。水稻是世界上最重要的粮食作物之一。然而，对水稻RNA结构的研究却很少。在这里，我们成功地在水稻中产生了体内Structure-seq文库。我们发现，mRNA的结构灵活性可能与生物功能的动力学。较高的N6-甲基腺苷（m6 A）修饰倾向于在3′ UTR中具有较少的RNA结构，而GC含量不会显著影响体内mRNA结构以维持有效的生物过程，如翻译。对水稻和拟南芥RNA结构组的比较分析表明，GC含量越高，RNA结构越不灵活。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的弱相关性。序列和体内RNA结构的保守性和差异性对应于不同的和特定的生物学过程。我们的研究结果表明，RNA二级结构可能提供了一个单独的选择层的单子叶植物和双子叶植物之间的序列。因此，我们的研究表明，RNA结构在不同的生物过程中进化不同，以保持在被子植物进化过程中的发展和适应灵活性的鲁棒性。本研究首次揭示了水稻体内高质量、高深度的RNA结构组。本研究首次比较了单子叶和双子叶模式植物体内的RNA结构组。体内RNA结构保守性/趋异性的全局比较表明，RNA二级结构可能为序列提供了一个单独的进化选择层。
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 N6-methyladenosine (m6A) 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. We have revealed the first rice in vivo RNA structurome with both high quality and depths. Our study for the first time compares in vivo RNA structurome between monocot and dicot model plant systems. The global comparison of in vivo RNA structure conservation/divergence indicates that RNA secondary structure might offer a separate layer of evolutionary selection to sequence.
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