A Comprehensive Map of Intron Branchpoints and Lariat RNAs in Plants
A Comprehensive Map of Intron Branchpoints and Lariat RNAs in Plants
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植物内含子分支点和套索 RNA 综合图谱
DOI：
10.1105/tpc.18.00711
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发表时间：
2019-05-01
期刊：
影响因子：
11.6
通讯作者：
Zheng，Yun
中科院分区：
文献类型：
--
作者：
Zhang，Xiaotuo;Zhang，Yong;Zheng，Yun
在剪接过程中，当5 '剪接位点与分枝点（BP）连接时，剪切的内含子形成分枝。虽然幼虫RNA通常被RNA脱分枝酶1降解，但最近在动物实验中发现了许多生理条件下的幼虫RNA。相比之下，bp的特征以及幼虫rna自然积累的程度在植物中基本上未被探索。在这里，我们分析了948个RNA测序数据集，在全基因组范围内记录了植物bp和分支RNA。在拟南芥（Arabidopsis thaliana）、番茄（Solanum lycopersicum）、水稻（Oryza sativa）和玉米（Zea mays）中分别鉴定出13872、5199、29,582和13478个bp。植物bp的特征与酵母菌和人的bp非常相似，bp具有腺嘌呤偏好，并且两侧有富含尿嘧啶的序列。有趣的是，约20%的内含子含有多个BP，并且BP的使用是组织特异性的。此外，野生型拟南芥植株中积累了10580个分枝rna，这些分枝rna大多来自较长的或缺乏逆转录元件的内含子。此外，这些分支rna的表达伴随着亲本外显子反剪接的发生。总的来说，我们的研究结果提供了四种植物物种中内含子bp和支链rna的综合图谱，并揭示了支链转换和剪接之间的联系。
Lariats are formed by excised introns, when the 5′ splice site joins with the branchpoint (BP) during splicing. Although lariat RNAs are usually degraded by RNA debranching enzyme 1, recent findings in animals detected many lariat RNAs under physiological conditions. By contrast, the features of BPs and to what extent lariat RNAs accumulate naturally are largely unexplored in plants. Here, we analyzed 948 RNA sequencing data sets to document plant BPs and lariat RNAs on a genome-wide scale. In total, we identified 13,872, 5199, 29,582, and 13,478 BPs in Arabidopsis (Arabidopsis thaliana), tomato (Solanum lycopersicum), rice (Oryza sativa), and maize (Zea mays), respectively. Features of plant BPs are highly similar to those in yeast and human, in that BPs are adenine-preferred and flanked by uracil-enriched sequences. Intriguingly, ∼20% of introns harbor multiple BPs, and BP usage is tissue-specific. Furthermore, 10,580 lariat RNAs accumulate in wild-type Arabidopsis plants, and most of these lariat RNAs originate from longer or retroelement-depleted introns. Moreover, the expression of these lariat RNAs is accompanied by the incidence of back-splicing of parent exons. Collectively, our results provide a comprehensive map of intron BPs and lariat RNAs in four plant species and uncover a link between lariat turnover and splicing.