Genome-Wide cis-Regulatory Element Based Discovery of Auxin-Responsive Genes in Higher Plant.
Genome-Wide cis-Regulatory Element Based Discovery of Auxin-Responsive Genes in Higher Plant.
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DOI：
10.3390/genes13010024
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发表时间：
2021-12-23
期刊：
影响因子：
3.5
通讯作者：
Zeng F
中科院分区：
文献类型：
--
作者：
Wu J;Gao F;Li T;Guo H;Zhang L;Fan Y;Chen A;Wang J;Shi F;Shan G;Guo H;Zeng F
生长素对植物生理有着深远的影响，几乎参与了植物发育过程的各个方面。生长素通过调控生长素应答基因的表达，对植物的生长和分化具有深远的多效性作用。经典的生长素反应通常是由生长素反应因子（auxin response factors, ARFs）介导的，它与靶基因启动子区的生长素反应元件（AuxRE）结合。实验只产生了有限数量的具有明确功能的植物基因。目前尚不清楚有多少基因对外源性生长素有反应。提出了一种经济有效的模式植物拟南芥（拟南芥）生长素应答基因全基因组发现方法。我们的方法依赖于在基因组中不同启动子中发现基于顺式调控元件的靶向基因。我们首先挖掘并分析了生长素特异性顺式调控元件对靶基因的转录，然后在拟南芥基因组超过25,800个启动子中鉴定出可能的生长素响应基因，其启动子包含这些元件。通过与已发表的数据库和文献进行比较，我们发现该方法预测生长素应答候选基因的准确率为65.2%（309/474）。本文还对预测的生长素应答基因的染色体分布和注释进行了挖掘。该结果可显著减少已鉴定但仅是潜在生长素靶基因的数量，并为改进缺乏功能信息的基因的注释提供有用的线索。
Auxin has a profound impact on plant physiology and participates in almost all aspects of plant development processes. Auxin exerts profound pleiotropic effects on plant growth and differentiation by regulating the auxin response genes’ expressions. The classical auxin reaction is usually mediated by auxin response factors (ARFs), which bind to the auxin response element (AuxRE) in the promoter region of the target gene. Experiments have generated only a limited number of plant genes with well-characterized functions. It is still unknown how many genes respond to exogenous auxin treatment. An economical and effective method was proposed for the genome-wide discovery of genes responsive to auxin in a model plant, Arabidopsis thaliana (A. thaliana). Our method relies on cis-regulatory-element-based targeted gene finding across different promoters in a genome. We first exploit and analyze auxin-specific cis-regulatory elements for the transcription of the target genes, and then identify putative auxin responsive genes whose promoters contain the elements in the collection of over 25,800 promoters in the A. thaliana genome. Evaluating our result by comparing with a published database and the literature, we found that this method has an accuracy rate of 65.2% (309/474) for predicting candidate genes responsive to auxin. Chromosome distribution and annotation of the putative auxin-responsive genes predicted here were also mined. The results can markedly decrease the number of identified but merely potential auxin target genes and also provide useful clues for improving the annotation of gene that lack functional information.
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