Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, North Carolina Research Campus, 600 Laureate Way, Kannapolis, NC 28081, USA.
BMC Plant Biol. 2010 Jun 4;10:102. doi: 10.1186/1471-2229-10-102.
Around 14% of protein-coding genes of Arabidopsis thaliana genes from the TAIR9 genome release are annotated as producing multiple transcript variants through alternative splicing. However, for most alternatively spliced genes in Arabidopsis, the relative expression level of individual splicing variants is unknown.
We investigated prevalence of alternative splicing (AS) events in Arabidopsis thaliana using ESTs. We found that for most AS events with ample EST coverage, the majority of overlapping ESTs strongly supported one major splicing choice, with less than 10% of ESTs supporting the minor form. Analysis of ESTs also revealed a small but noteworthy subset of genes for which alternative choices appeared with about equal prevalence, suggesting that for these genes the variant splicing forms co-occur in the same cell types. Of the AS events in which both forms were about equally prevalent, more than 80% affected untranslated regions or involved small changes to the encoded protein sequence.
Currently available evidence from ESTs indicates that alternative splicing in Arabidopsis occurs and affects many genes, but for most genes with documented alternative splicing, one AS choice predominates. To aid investigation of the role AS may play in modulating function of Arabidopsis genes, we provide an on-line resource (ArabiTag) that supports searching AS events by gene, by EST library keyword search, and by relative prevalence of minor and major forms.
在拟南芥 TAIR9 基因组版本中，约有 14%的蛋白质编码基因通过选择性剪接被注释为产生多个转录变体。然而，对于拟南芥中大多数选择性剪接的基因，其个别剪接变体的相对表达水平是未知的。
我们使用 EST 来研究拟南芥中选择性剪接（AS）事件的普遍性。我们发现，对于大多数具有充足 EST 覆盖的 AS 事件，大多数重叠的 EST 强烈支持一种主要的剪接选择，只有不到 10%的 EST 支持次要形式。EST 的分析还揭示了一小部分但值得注意的基因，其替代选择似乎具有同等的普遍性，这表明对于这些基因，变体剪接形式在相同的细胞类型中共同出现。在两种形式同等普遍的 AS 事件中，超过 80%的事件影响非翻译区或涉及编码蛋白序列的微小变化。
目前来自 EST 的证据表明，拟南芥中的选择性剪接确实发生，并影响许多基因，但对于大多数有记录的选择性剪接基因，一种 AS 选择占主导地位。为了帮助研究选择性剪接在调节拟南芥基因功能方面可能发挥的作用，我们提供了一个在线资源（ArabiTag），该资源支持按基因、按 EST 文库关键字搜索以及按次要和主要形式的相对普遍性来搜索 AS 事件。
