Institute of Plant and Microbial Biology, Academia Sinica, 11529 Taipei, Taiwan.
Plant Physiol. 2013 Jul;162(3):1750-63. doi: 10.1104/pp.113.217778. Epub 2013 Jun 4.
Iron (Fe) deficiency is a world-wide nutritional disorder in both plants and humans, resulting from its restricted bioavailability for plants and, subsequently, low Fe concentration in edible plant parts. Plants have evolved sophisticated mechanisms to alleviate Fe deficiency, with the aim of recalibrating metabolic fluxes and maintaining cellular Fe homeostasis. To analyze condition-sensitive changes in precursor mRNA (pre-mRNA) splicing pattern, we mapped the transcriptome of Fe-deficient and Fe-sufficient Arabidopsis (Arabidopsis thaliana) roots using the RNA sequencing technology and a newly developed software toolbox, the Read Analysis & Comparison Kit in Java (RACKJ). In alternatively spliced genes, stress-related Gene Ontology categories were overrepresented, while housekeeping cellular functions were mainly transcriptionally controlled. Fe deficiency increased the complexity of the splicing pattern and triggered the differential alternative splicing of 313 genes, the majority of which had differentially retained introns. Several genes with important functions in Fe acquisition and homeostasis were both differentially expressed and differentially alternatively spliced upon Fe deficiency, indicating a complex regulation of gene activity in Fe-deficient conditions. A comparison with a data set for phosphate-deficient plants suggests that changes in splicing patterns are nutrient specific and not or not chiefly caused by stochastic fluctuations. In sum, our analysis identified extensive posttranscriptional control, biasing the abundance and activity of proteins in a condition-dependent manner. The production of a mixture of functional and nonfunctional transcripts may provide a means to fine-tune the abundance of transcripts with critical importance in cellular Fe homeostasis. It is assumed that differential gene expression and nutrient deficiency-induced changes in pre-mRNA splicing represent parallel, but potentially interacting, regulatory mechanisms.
铁（Fe）缺乏是植物和人类中一种全球性的营养失调，源于其对植物的生物利用度有限，从而导致可食用植物部分的铁含量低。植物已经进化出复杂的机制来缓解铁缺乏，目的是重新校准代谢通量并维持细胞内铁稳态。为了分析前体 mRNA（pre-mRNA）剪接模式的条件敏感性变化，我们使用 RNA 测序技术和新开发的软件工具箱，即 Java 中的 Read Analysis & Comparison Kit（RACKJ），对缺铁和铁充足的拟南芥（Arabidopsis thaliana）根进行了转录组映射。在选择性剪接基因中，应激相关的基因本体论（GO）类别过度表达，而管家细胞功能主要通过转录调控。铁缺乏增加了剪接模式的复杂性，并触发了 313 个基因的差异选择性剪接，其中大多数基因具有差异保留的内含子。在铁缺乏时，一些在铁获取和稳态中具有重要功能的基因既表现出差异表达，也表现出差异选择性剪接，表明在铁缺乏条件下对基因活性进行了复杂的调控。与磷酸盐缺乏植物的数据集进行比较表明，剪接模式的变化是特定于营养物质的，而不是或主要不是由随机波动引起的。总之，我们的分析确定了广泛的转录后调控，以条件依赖的方式偏置蛋白质的丰度和活性。产生功能性和非功能性转录本的混合物可能提供了一种微调对细胞内铁稳态至关重要的转录本丰度的方法。据假设，差异基因表达和营养缺乏诱导的 pre-mRNA 剪接变化代表平行但潜在相互作用的调节机制。
