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Genomewide comparative analysis of alternative splicing in plants

机译：全基因组植物中选择性剪接的比较分析

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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).
机译：选择性剪接（AS）在哺乳动物系统中已得到广泛研究，但在植物中却很少。在这里，我们报告从EST / cDNA分析推断出的两种AS植物事件：拟南芥和水稻。在拟南芥中，有EST / cDNA证据的基因中有4,707（21.8％）个基因显示8,264 AS事件。这些事件中约有56％是内含子保留（IntronR），只有8％是外显子跳跃。在水稻中，有6568个（21.2％）表达的基因显示14542个AS事件，其中53.5％是IntronR，13.8％是外显子跳跃。一致的IntronR高频提示通过植物中的内含子定义普遍存在剪接位点识别。给定基因内的不同AS事件在很大程度上独立发生。总体而言，如果该事件在植物中像在人类中一样起作用，则36-43％的AS事件产生的转录本将成为无义介导的衰变途径的靶标。水稻中也剪接了40％的拟南芥AS基因，其中一些例子强烈暗示了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Web界面数据库，以汇编和可视化植物替代剪接的证据（植物替代剪接，可从www.plantgdb.org/ASIP获得）。

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