Deciphering the role of RNA structure in translation efficiency.
Deciphering the role of RNA structure in translation efficiency.
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DOI：
10.1186/s12859-022-05037-7
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发表时间：
2022-12-23
影响因子：
3
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中科院分区：
文献类型：
--
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RNA二级结构对RNA代谢的命运有着广泛的影响。编码区翻译起始点/起始密码子附近二级结构稳定性的降低提高了原核生物和真核生物的翻译效率。然而，In Silo折叠的不准确性和对编码区的关注限制了我们对整个mRNA结构与翻译效率之间的全球关系的理解。利用转录组中高通量的RNA结构探测数据，我们旨在系统地研究RNA结构在调节翻译效率中的作用。在这里，我们分析了数百种序列和结构特征对小鼠胚胎干细胞(MESCs)和斑马鱼发育阶段翻译效率的影响。我们的发现表明，在mESCs和斑马鱼中，整体体内RNA结构在预测翻译效率方面比体外RNA结构具有更高的相对重要性。此外，与编码区或5‘非翻译区的RNA结构相比，3’非翻译区的RNA结构对翻译效率的影响要强得多。此外，在mESCs的高翻译mRNAs中检测到体外和体内结构之间的强烈交替，但在斑马鱼中检测到高翻译的mRNAs。相反，在斑马鱼的高翻译mRNAs中检测到5‘非编码区和近端编码区的体外和体内RNA结构之间的适度变化。我们的结果表明，3‘非编码区的开放促进了小鼠和斑马鱼的翻译效率，其中3’非编码区的体内结构在小鼠中比在斑马鱼中更重要。这揭示了RNA二级结构在翻译调控中的新作用。网上版载有补充材料，可在10.1186/s12859-022-05037-7查阅。
RNA secondary structure has broad impact on the fate of RNA metabolism. The reduced stability of secondary structures near the translation initiation site/start codon of the coding region promotes the efficiency of translation in both prokaryotic and eukaryotic species. However, the inaccuracy of in silico folding and the focus on the coding region limit our understanding of the global relationship between the whole mRNA structure and translation efficiency. Leveraging high-throughput RNA structure probing data in the transcriptome, we aim to systematically investigate the role of RNA structure in regulating translation efficiency. Here, we analyze the influences of hundreds of sequence and structural features on translation efficiency in the mouse embryonic stem cells (mESCs) and zebrafish developmental stages. Our findings reveal that overall in vivo RNA structure has a higher relative importance in predicting translation efficiency than in vitro RNA structure in both mESCs and zebrafish. Also, RNA structures in 3’ untranslated region (UTR) have much stronger influence on translation efficiency compared to those in coding regions or 5' UTR. Furthermore, strong alternation between in vitro and in vivo structures in 3' UTR are detected in highly translated mRNAs in mESCs but not zebrafish. Instead, moderate alteration between in vitro and in vivo RNA structures in the 5’ UTR and proximal coding regions are detected in highly translated mRNAs in zebrafish. Our results suggest the openness of the 3’ UTR promotes the translation efficiency in both mice and zebrafish, with the in vivo structure in 3’ UTR more important in mice than in zebrafish. This reveals a novel role of RNA secondary structure on translational regulation. The online version contains supplementary material available at 10.1186/s12859-022-05037-7.
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影响因子：
7
作者：
Hausser J;Syed AP;Bilen B;Zavolan M
通讯作者：
Zavolan M
原核生物和真核生物翻译起始位点附近 mRNA 稳定性降低的普遍趋势
影响因子：
4.3
作者：
Gu W;Zhou T;Wilke CO
通讯作者：
Wilke CO
影响因子：
4
作者：
Preiss, T;Hentze, MW
通讯作者：
Hentze, MW
DOI：
10.1016/j.bbrc.2020.05.170
发表时间：
2020-08-27
影响因子：
3.1
作者：
Guo, Shuangshuang;Lv, Chunyu;Yuan, Shuiqiao
通讯作者：
Yuan, Shuiqiao
影响因子：
2.9
作者：
MCCASKILL, JS
通讯作者：
MCCASKILL, JS