Article type : Resource Genome-wide analysis of specific alterations in transcript structure and accumulation caused by nutrient deficiencies in Arabidopsis thaliana
Article type : Resource Genome-wide analysis of specific alterations in transcript structure and accumulation caused by nutrient deficiencies in Arabidopsis thaliana
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发表时间：
2017
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通讯作者：
S. Nishida;Yusuke Kakei;Y. Shimada;T. Fujiwara
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作者：
S. Nishida;Yusuke Kakei;Y. Shimada;T. Fujiwara
转录本结构的改变有助于转录组的可塑性。在这项研究中，我们分析了外显子组合模式对拟南芥根中 12 种不同营养素缺乏的全基因组响应。 RNA 测序分析和生物信息学利用模拟调查揭示了 600 多个基因，显示出不同的外显子组合。显示差异表达（DE）的基因和显示差异外显子组合（DC）的基因之间的重叠显着较小。此外，基因本体分析表明，DE 和 DC 基因之间的基因功能不共享，这表明显示 DC 的基因与显示 DE 的基因具有不同的作用。大多数 DC 基因具有营养特异性。例如，MYB 转录因子基因 MYB48 和 MYB59 的两个同源物仅在响应低 K 时表现出差异性选择性剪接。这些 MYB 基因的选择性剪接调节 DNA 结合基序，据报道 MYB59 参与抑制根伸长。因此，低 K 下具有完整 DNA 结合基序的 MYB 亚型丰度增加可能与根伸长的主动抑制有关。总体而言，我们提供了受营养缺乏影响的 DC 基因的全球综合数据，这有助于揭示适应营养状况的未知机制。
Alteration of transcript structure contributes to transcriptome plasticity. In this study, we analyzed the genome-wide response of exon combination patterns to deficiencies in 12 different nutrients in Arabidopsis thaliana roots. RNA sequencing analysis and bioinformatics using a simulation survey revealed more than 600 genes showing varying exon combinations. The overlap between genes showing differential expression (DE) and genes showing differential exon combination (DC) was significantly small. Additionally, gene ontology analysis showed that gene functions were not shared between the DE and DC genes, suggesting that the genes showing DC had different roles than those showing DE. Most of the DC genes were nutrient-specific. For example, two homologs of the MYB transcription factor genes MYB48 and MYB59 showed differential alternative splicing only in response to low K. Alternative splicing of those MYB genes modulated DNA-binding motifs, and MYB59 is reportedly involved in the inhibition of root elongation. Therefore, the increased abundance of MYB isoforms with an intact DNA-binding motif under low K may be involved in the active inhibition of root elongation. Overall, we provide global and comprehensive data of DC genes affected by nutritional deficiencies, which contribute to uncover an unknown mechanism involved in the adaptation to nutrient status.