Genome-wide mapping of alternative splicing in Arabidopsis thaliana
Genome-wide mapping of alternative splicing in Arabidopsis thaliana
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DOI：
10.1101/gr.093302.109
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发表时间：
2010-01-01
期刊：
影响因子：
7
通讯作者：
Mockler, Todd C.
中科院分区：
文献类型：
--
作者：
Filichkin, Sergei A.;Priest, Henry D.;Mockler, Todd C.
选择性剪接可以提高转录组的可塑性和蛋白质组的多样性。在植物中，选择性剪接可以在不同的发育阶段表现出来，并且通常与特定的组织类型或环境条件（如非生物胁迫）有关。我们使用Illumina超高通量RNA测序（RNA-seq）平台以单碱基分辨率绘制拟南芥转录组图谱。深度转录组测序证实了大多数带注释的内含子，并鉴定了数千种新的可选剪接的mRNA亚型。我们的分析表明，拟南芥中至少有42%的内含子基因是选择性剪接的；这明显高于先前基于cDNA/表达序列标签测序的估计。随机验证证实，通过RNA-seq经验预测的新的剪接异构体可以在体内检测到。RNA-seq检测到的新内含子在非一致末端二核苷酸剪接信号中大量富集。具有过早终止密码子（ptc）的选择性异构体构成了大部分的选择性剪接转录本。以一个重要的生物钟基因为例，我们发现内含子保留可以产生相对丰富的PTC+异构体，并且这一特定事件在不同植物物种中高度保守。选择性剪接的PTC+亚型可以成为无义介导的mRNA衰变（NMD）监测机制降解的潜在目标，或者通过调节非生产性剪接和翻译（RUST）机制调节功能转录物的水平。我们证明，在非生物胁迫处理下，几个关键调控基因的PTC+和参考异构体的相对比例可以显著改变。综上所述，我们的研究结果表明，与动物一样，NMD和RUST可能在植物中广泛存在，并可能在调节基因表达方面发挥重要作用。
Alternative splicing can enhance transcriptome plasticity and proteome diversity. In plants, alternative splicing can be manifested at different developmental stages, and is frequently associated with specific tissue types or environmental conditions such as abiotic stress. We mapped the Arabidopsis transcriptome at single-base resolution using the Illumina platform for ultrahigh-throughput RNA sequencing (RNA-seq). Deep transcriptome sequencing confirmed a majority of annotated introns and identified thousands of novel alternatively spliced mRNA isoforms. Our analysis suggests that at least similar to 42% of intron-containing genes in Arabidopsis are alternatively spliced; this is significantly higher than previous estimates based on cDNA/expressed sequence tag sequencing. Random validation confirmed that novel splice isoforms empirically predicted by RNA-seq can be detected in vivo. Novel introns detected by RNA-seq were substantially enriched in non-consensus terminal dinucleotide splice signals. Alternative isoforms with premature termination codons (PTCs) comprised the majority of alternatively spliced transcripts. Using an example of an essential circadian clock gene, we show that intron retention can generate relatively abundant PTC+ isoforms and that this specific event is highly conserved among diverse plant species. Alternatively spliced PTC+ isoforms can be potentially targeted for degradation by the nonsense mediated mRNA decay (NMD) surveillance machinery or regulate the level of functional transcripts by the mechanism of regulated unproductive splicing and translation (RUST). We demonstrate that the relative ratios of the PTC+ and reference isoforms for several key regulatory genes can be considerably shifted under abiotic stress treatments. Taken together, our results suggest that like in animals, NMD and RUST may be widespread in plants and may play important roles in regulating gene expression.