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Rice in vivo RNA Structurome Reveals RNA Secondary Structure Conservation and Divergence in plants
Hongjing Deng, Jitender Cheema, Hang Zhang, Hugh Woolfenden, Matthew Norris, Zhenshan Liu, Qi Liu, Xiaofei Yang, Minglei Yang, Xian Deng, Xiaofeng Cao and Yiliang Ding
Molecular Plant
Abstract
RNA secondary structure plays a critical role in gene regulation. Rice (Oryza sativa L.) is one of the most important food crops in the world. However, RNA structure in rice has scarcely been studied. Here, for the first time 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. 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. We also 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 sequence between monocot and dicot. Therefore, our study implies that RNA structure evolves differently for various biological processes to maintain robustness in development and flexibility in adaptation during angiosperm evolution.
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论文编号: |
DOI:10.1016/j.molp.2018.01.008 |
论文题目: |
Rice in vivo RNA Structurome Reveals RNA Secondary Structure Conservation and Divergence in plants |
英文论文题目: |
Rice in vivo RNA Structurome Reveals RNA Secondary Structure Conservation and Divergence in plants |
第一作者: |
Hongjing Deng, Jitender Cheema, Hang Zhang, Hugh Woolfenden, Matthew Norris, Zhenshan Liu, Qi Liu, Xiaofei Yang, Minglei Yang, Xian Deng, Xiaofeng Cao and Yiliang Ding |
英文第一作者: |
Hongjing Deng, Jitender Cheema, Hang Zhang, Hugh Woolfenden, Matthew Norris, Zhenshan Liu, Qi Liu, Xiaofei Yang, Minglei Yang, Xian Deng, Xiaofeng Cao and Yiliang Ding |
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2018-02-05 |
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摘要: |
RNA secondary structure plays a critical role in gene regulation. Rice (Oryza sativa L.) is one of the most important food crops in the world. However, RNA structure in rice has scarcely been studied. Here, for the first time 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. 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. We also 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 sequence between monocot and dicot. Therefore, our study implies that RNA structure evolves differently for various biological processes to maintain robustness in development and flexibility in adaptation during angiosperm evolution. |
英文摘要: |
RNA secondary structure plays a critical role in gene regulation. Rice (Oryza sativa L.) is one of the most important food crops in the world. However, RNA structure in rice has scarcely been studied. Here, for the first time 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. 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. We also 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 sequence between monocot and dicot. Therefore, our study implies that RNA structure evolves differently for various biological processes to maintain robustness in development and flexibility in adaptation during angiosperm evolution. |
刊物名称: |
Molecular Plant |
英文刊物名称: |
Molecular Plant |
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其它备注: |
Hongjing Deng, Jitender Cheema, Hang Zhang, Hugh Woolfenden, Matthew Norris, Zhenshan Liu, Qi Liu, Xiaofei Yang, Minglei Yang, Xian Deng, Xiaofeng Cao, Yiliang Ding. Rice in vivo RNA Structurome Reveals RNA Secondary Structure Conservation and Divergence in plants. Molecular Plant. DOI:10.1016/j.molp.2018.01.008 |
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