State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China.
Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan 650500, China.
Plant Cell. 2019 May;31(5):956-973. doi: 10.1105/tpc.18.00711. Epub 2019 Mar 20.
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 (), tomato (), rice (), and maize (), 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.
套索由切除的内含子形成，当 5'剪接位点在剪接过程中与分支点（BP）结合时。尽管套索 RNA 通常被 RNA 分支酶 1 降解，但动物最近的发现表明，在生理条件下存在许多套索 RNA。相比之下，BP 的特征以及套索 RNA 自然积累的程度在植物中还没有得到充分探索。在这里，我们分析了 948 个 RNA 测序数据集，以在全基因组范围内记录植物的 BP 和套索 RNA。总的来说，我们分别在拟南芥（Arabidopsis）、番茄（tomato）、水稻（rice）和玉米（maize）中鉴定了 13872、5199、29582 和 13478 个 BP。植物 BP 的特征与酵母和人类的特征非常相似，即 BP 是腺嘌呤偏好的，并且被富含尿嘧啶的序列侧翼。有趣的是，约 20%的内含子含有多个 BP，并且 BP 的使用具有组织特异性。此外，在野生型拟南芥植物中积累了 10580 个套索 RNA，其中大多数套索 RNA 来自更长或缺少逆转录元件的内含子。此外，这些套索 RNA 的表达伴随着亲本外显子反向剪接的发生。总的来说，我们的结果提供了四个植物物种中内含子 BP 和套索 RNA 的综合图谱，并揭示了套索周转和剪接之间的联系。
