In vivo nuclear RNA structurome reveals RNA-structure regulation of mRNA processing in plants.
In vivo nuclear RNA structurome reveals RNA-structure regulation of mRNA processing in plants.
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DOI：
10.1186/s13059-020-02236-4
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发表时间：
2021-01-04
期刊：
影响因子：
12.3
通讯作者：
Ding Y
中科院分区：
文献类型：
--
作者：
Liu Z;Liu Q;Yang X;Zhang Y;Norris M;Chen X;Cheema J;Zhang H;Ding Y
mRNA加工对基因表达至关重要。调节mRNA加工的一个挑战是如何识别实际的mRNA加工位点，如剪接和多聚腺苷酸化位点，当序列含量不足以达到此目的时。以前的研究表明，RNA结构影响mRNA的加工。然而，RNA结构在mRNA加工中的调节作用仍不清楚。在这里，我们进行了体内选择性2′-羟基酰化分析引物延伸（SHAPE）化学分析拟南芥，并产生在体内核RNA结构的景观。我们发现，核mRNA折叠不同的跨翻译起始和终止位点的胞质mRNA。值得注意的是，我们发现了一个两个核苷酸的单链RNA结构特征上游的5′剪接位点，这是密切相关的剪接和选择的5′剪接位点。这种RNA结构特征的调节作用通过实验验证得到进一步证实。此外，我们发现分支位点的单链性也与3′剪接位点的识别有关。我们还确定了一个RNA结构特征，包括两个密切的单链区域，这是专门与多聚腺苷酸化和替代多聚腺苷酸化事件。我们成功地确定了前mRNA的结构特征与剪接和多聚腺苷酸化在全基因组规模和验证的RNA结构特征，可以调节剪接。我们的研究揭示了一个新的RNA结构调控机制的mRNA加工。
mRNA processing is critical for gene expression. A challenge in regulating mRNA processing is how to recognize the actual mRNA processing sites, such as splice and polyadenylation sites, when the sequence content is insufficient for this purpose. Previous studies suggested that RNA structure affects mRNA processing. However, the regulatory role of RNA structure in mRNA processing remains unclear. Here, we perform in vivo selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE) chemical profiling on Arabidopsis and generate the in vivo nuclear RNA structure landscape. We find that nuclear mRNAs fold differently from cytosolic mRNAs across translation start and stop sites. Notably, we discover a two-nucleotide single-stranded RNA structure feature upstream of 5′ splice sites that is strongly associated with splicing and the selection of alternative 5′ splice sites. The regulatory role of this RNA structure feature is further confirmed by experimental validation. Moreover, we find the single-strandedness of branch sites is also associated with 3′ splice site recognition. We also identify an RNA structure feature comprising two close-by single-stranded regions that is specifically associated with both polyadenylation and alternative polyadenylation events. We successfully identify pre-mRNA structure features associated with splicing and polyadenylation at whole-genome scale and validate an RNA structure feature which can regulate splicing. Our study unveils a new RNA structure regulatory mechanism for mRNA processing.
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