Comprehensive discovery of salt-responsive alternative splicing events based on Iso-Seq and RNA-seq in grapevine roots
Comprehensive discovery of salt-responsive alternative splicing events based on Iso-Seq and RNA-seq in grapevine roots
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基于Iso-Seq和RNA-seq全面发现葡萄根中盐响应选择性剪接事件
DOI：
10.1016/j.envexpbot.2021.104645
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发表时间：
2021-12
影响因子：
5.7
通讯作者：
Yuxin Yao
中科院分区：
文献类型：
--
作者：
Zhongxin Jin;Xinning Lv;Yushuai Sun;Zongbao Fan;Guangqing Xiang;Yuxin Yao
选择性剪接(AS)可以通过转录组的可塑性来增强生物体对非生物胁迫的适应能力；然而，在葡萄根中，AS事件对盐的反应机制尚不清楚。在本研究中，利用葡萄根部的Iso-Seq和RNA-Seq数据生成了优化的基因组注释文件。根据更新的文件，在A17个葡萄根中共鉴定出5种类型的8,453个AS事件，其中保留内含子(RI)是最主要的类型。共有1,466个AS事件与1,113个基因相关，它们对葡萄根中的盐胁迫做出了反应。包裹体异构体的比例在全球范围内呈下降趋势，表明盐胁迫促进了较短异构体的产生。只有206个盐响应AS事件与差异表达的基因有关，这表明转录调控和转录后调控之间几乎没有重叠。共有672个和410个AS事件分别影响蛋白质产物的长度和miRNA结合。差异剪接基因主要与RNA加工、核酸结合和离子通道活性有关。此外，还鉴定了盐诱导的剪接体蛋白基因LSM2和SRSF1，并推测了它们在调节AS事件中的可能作用。此外，我们起草了一种方法，利用Iso-Seq数据来探索AS和替代聚腺苷酸化(APA)之间可能的相互作用。总体而言，这些发现提供了对葡萄根中盐响应AS事件的全面了解，为葡萄耐盐的分子机制提供了洞察。
Alternative splicing (AS) can enhance the adaptive capacity of organisms to respond to abiotic stresses via transcriptome plasticity; however, the mechanism underlying the responses of AS events to salt remains unclear in grapevine roots. In this study, an optimized genome annotation file was generated using Iso-Seq and RNA-seq data of grapevine roots. Based on the updated file, a total of 8,453 AS events across five types were identified in A17 grapevine roots, of which retained intron (RI) was the most dominant type. A total of 1,466 AS events affiliated with 1,113 genes responded to salt stress in grapevine roots. A global decrease in the proportion of inclusion isoforms was demonstrated, indicating that salt stress promoted the production of shorter isoforms. Only 206 salt-responsive AS events were affiliated with differentially expressed genes, indicating little overlap between transcriptional regulation and post-transcriptional regulation. A total of 672 and 410 AS events affected the length of protein products and miRNA binding, respectively. Differentially spliced genes were primarily related to RNA processing, nucleic acid binding, and ion channel activity. In addition, the salt-induced spliceosomal protein genesLSM2andSRSF1were identified, and their possible roles in regulating AS events were inferred. Moreover, we drafted an approach to explore possible interactions between AS and alternative polyadenylation (APA) using Iso-Seq data. Overall, these findings provide a comprehensive understanding of salt-responsive AS events in grapevine roots, providing insight into the molecular mechanism of salt tolerance in grapevine.
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影响因子：
3.5
作者：
Jiwoong Wi;Yeonju Na;E. Yang;Jung-Hyun Lee;W. Jeong;D. Choi
通讯作者：
Jiwoong Wi;Yeonju Na;E. Yang;Jung-Hyun Lee;W. Jeong;D. Choi
影响因子：
16.6
作者：
Abdel-Ghany SE;Hamilton M;Jacobi JL;Ngam P;Devitt N;Schilkey F;Ben-Hur A;Reddy AS
通讯作者：
Reddy AS
影响因子：
5.3
作者：
Losada JM;Herrero M
通讯作者：
Herrero M
DOI：
10.1073/pnas.2018251118
发表时间：
2021-04-06
影响因子：
11.1
作者：
Aubol, Brandon E.;Wozniak, Jacob M.;Adams, Joseph A.
通讯作者：
Adams, Joseph A.
葡萄环状RNA的表征和克隆鉴定出抗寒相关的Vv-circATS1
影响因子：
7.4
作者：
Gao, Zhen;Li, Jing;Ma, Chao
通讯作者：
Ma, Chao