Genomewide comparative analysis of alternative splicing in plants
Genomewide comparative analysis of alternative splicing in plants
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DOI：
10.1073/pnas.0602039103
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发表时间：
2006-05-02
影响因子：
11.1
通讯作者：
Brendel, V
中科院分区：
文献类型：
--
作者：
Wang, BB;Brendel, V
选择性剪接（AS）在哺乳动物系统中得到了广泛的研究，但在植物中的研究却少之又少。在这里，我们报告了两种模式植物（拟南芥和水稻）中 EST/cDNA 分析推导出的 AS 事件。在拟南芥中，4,707 个 (21.8%) 具有 EST/cDNA 证据的基因显示 8,264 个 AS 事件。这些事件中大约 56% 是内含子保留 (IntronR)，只有 8% 是外显子跳跃。在水稻中，6,568 个（21.2%）表达基因显示 14,542 个 AS 事件，其中 53.5% 是内含子 R，13.8% 是外显子跳跃。 IntronR 的一致高频率表明植物中通过内含子定义识别剪接位点的普遍性。给定基因内的不同 AS 事件大多数情况下是独立发生的。总共，36-43% 的 AS 事件产生的转录本将成为非意义介导的衰变途径的目标，如果该途径在植物中像在人类中一样发挥作用的话。 40% 的拟南芥 AS 基因也在水稻中进行选择性剪接，一些例子强烈表明 AS 事件作为转录后调控的进化保守机制的作用。我们创建了一个全面的网络接口数据库来编译和可视化植物中选择性剪接的证据（植物中的选择性剪接，可在 www.plantgdb.org/ASIP 上获取）。
Alternative splicing (AS) has been extensively studied in mammalian systems but much less in plants. Here we report AS events deduced from EST/cDNA analysis in two model plants: Arabidopsis and rice. In Arabidopsis, 4,707 (21.8%) of the genes with EST/cDNA evidence show 8,264 AS events. Approximately 56% of these events are intron retention (IntronR), and only 8% are exon skipping. In rice, 6,568 (21.2%) of the expressed genes display 14,542 AS events, of which 53.5% are IntronR and 13.8% are exon skipping. The consistent high frequency of IntronR suggests prevalence of splice site recognition by intron definition in plants. Different AS events within a given gene occur, for the most part, independently. In total, 36-43% of the AS events produce transcripts that would be targets of the non-sense-mediated decay pathway, if that pathway were to operate in plants as in humans. Forty percent of Arabidopsis AS genes are alternatively spliced also in rice, with some examples strongly suggesting a role of the AS event as an evolutionary conserved mechanism of post-transcriptional regulation. We created a comprehensive web-interfaced database to compile and visualize the evidence for alternative splicing in plants (Alternative Splicing in Plants, available at www.plantgdb.org/ASIP).