A high quality Arabidopsis transcriptome for accurate transcript-level analysis of alternative splicing.
A high quality Arabidopsis transcriptome for accurate transcript-level analysis of alternative splicing.
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DOI：
10.1093/nar/gkx267
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发表时间：
2017-05-19
影响因子：
14.9
通讯作者：
Brown JWS
中科院分区：
文献类型：
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作者：
Zhang R;Calixto CPG;Marquez Y;Venhuizen P;Tzioutziou NA;Guo W;Spensley M;Entizne JC;Lewandowska D;Ten Have S;Frei Dit Frey N;Hirt H;James AB;Nimmo HG;Barta A;Kalyna M;Brown JWS
选择性剪接产生来自同一基因的多个转录物和蛋白质亚型，因此在基因表达调控中具有重要意义。迄今为止，rna测序（RNA-seq）是在全基因组范围内量化选择性剪接变化的标准方法。了解RNA-seq目前的局限性对于可靠的分析至关重要，缺乏高质量、全面的大多数物种转录组，包括拟南芥等模式生物，是准确定量转录异构体的主要制约因素。为了解决这个问题，我们设计了一个具有严格过滤器的新管道，并组装了一个全面的拟南芥参考转录本数据集（AtRTD2），其中包含来自34 212个基因的82,190个非冗余转录本。广泛的实验验证表明，AtRTD2及其修饰版本AtRTD2- quasi用于可选剪接异构体的定量，在RNA-seq分析中优于其他可用的转录组。这种策略可以在其他物种中实施，以建立转录水平表达和选择性剪接分析的管道。
Alternative splicing generates multiple transcript and protein isoforms from the same gene and thus is important in gene expression regulation. To date, RNA-sequencing (RNA-seq) is the standard method for quantifying changes in alternative splicing on a genome-wide scale. Understanding the current limitations of RNA-seq is crucial for reliable analysis and the lack of high quality, comprehensive transcriptomes for most species, including model organisms such as Arabidopsis, is a major constraint in accurate quantification of transcript isoforms. To address this, we designed a novel pipeline with stringent filters and assembled a comprehensive Reference Transcript Dataset for Arabidopsis (AtRTD2) containing 82,190 non-redundant transcripts from 34 212 genes. Extensive experimental validation showed that AtRTD2 and its modified version, AtRTD2-QUASI, for use in Quantification of Alternatively Spliced Isoforms, outperform other available transcriptomes in RNA-seq analysis. This strategy can be implemented in other species to build a pipeline for transcript-level expression and alternative splicing analyses.