State Key Laboratory of Genetic Engineering and Institute of Plant Biology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University Shanghai, China ; Institutes of Biomedical Sciences, Fudan University Shanghai, China.
State Key Laboratory of Genetic Engineering and Institute of Plant Biology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University Shanghai, China.
Front Genet. 2014 Feb 12;5:25. doi: 10.3389/fgene.2014.00025. eCollection 2014.
Alternative splicing (AS) is a process in eukaryotic gene expression, in which the primary transcript of a multi-exon gene is spliced into two or more different mature transcripts, thereby increasing proteome diversity. AS is often regulated differentially between different tissues or developmental stages. Recent studies suggested that up to 60% of intron-containing genes in Arabidopsis thaliana undergo AS. Yet little is known about this complicated and important process during floral development. To investigate the preferential expression of different isoforms of individual alternatively spliced genes, we used high throughput RNA-Seq technology to explore the transcriptomes of three floral development stages of Arabidopsis thaliana and obtained information of various AS events. We identified approximately 24,000 genes that were expressed at one or more of these stages, and found that nearly 25% of multi-exon genes had two or more spliced variants. This is less frequent than the previously reported 40-60% for multiple organs and stages of A. thaliana, indicating that many genes expressed in floral development function with a single predominant isoform. On the other hand, 1716 isoforms were differentially expressed between the three stages, suggesting that AS might still play important roles in stage transition during floral development. Moreover, 337 novel transcribed regions were identified and most of them have a single exon. Taken together, our analyses provide a comprehensive survey of AS in floral development and facilitate further genomic and genetic studies.
可变剪接（AS）是真核生物基因表达过程中的一种机制，在此过程中，多外显子基因的初级转录本被剪接成两个或更多不同的成熟转录本，从而增加蛋白质组的多样性。AS 通常在不同组织或发育阶段之间存在差异调控。最近的研究表明，拟南芥中多达 60%的内含子基因发生 AS。然而，人们对这个复杂而重要的花发育过程知之甚少。为了研究不同组织中单个可变剪接基因的不同异构体的优先表达，我们使用高通量 RNA-Seq 技术来探索拟南芥三个花发育阶段的转录组，并获得了各种 AS 事件的信息。我们鉴定了大约 24000 个在一个或多个这些阶段表达的基因，发现近 25%的多外显子基因有两个或更多的剪接变体。这比之前报道的拟南芥多个器官和发育阶段的 40-60%要少，表明许多在花发育中表达的基因以单个主要异构体发挥功能。另一方面，在三个阶段之间有 1716 个异构体差异表达，这表明 AS 可能仍然在花发育过程中的阶段转换中发挥重要作用。此外，鉴定了 337 个新的转录区域，它们大多数只有一个外显子。总之，我们的分析提供了花发育中 AS 的全面调查，为进一步的基因组和遗传研究提供了便利。
