Common stress transcriptome analysis reveals functional and genomic architecture differences between early and delayed response genes

Chung Wen Lin, Li Yao Huang, Chao-Li Huang, Yong Chuan Wang, Pei Hsuan Lai, Hao-Ven Wang, Wen-Chi Chang, Tzen-Yuh Chiang, Hao-Jen Huang

研究成果: Article

4 引文 斯高帕斯(Scopus)

摘要

To identify the similarities among responses to diverse environmental stresses, we analyzed the transcriptome response of rice roots to three rhizotoxic perturbations (chromium, ferulic acid and mercury) and identified common early-transient, early-constant and delayed gene inductions. Common early response genes were mostly associated with signal transduction and hormones, and delayed response genes with lipid metabolism. Network component analysis revealed complicated interactions among common genes, the most highly connected signaling hubs being PP2C68, MPK5, LRR-RLK and NPR1. Gene architecture studies revealed different conserved promoter motifs and a different ratio of CpG island distribution between early and delayed genes. In addition, early-transient genes had more exons and a shorter first exon. IMEter was used to calculate the transcription regulation effects of introns, with greater effects for the first introns of early-transient than delayed genes. The higher Ka/Ks (non-synonymous/ synonymous mutation) ratio of early-constant genes than early-transient, delayed and the genome median demonstrates the rapid evolution of early-constant genes. Our results suggest that finely tuned transcriptional control in response to environmental stress in rice depends on genomic architecture and signal intensity and duration.

原文English
頁(從 - 到)546-559
頁數14
期刊Plant and Cell Physiology
58
發行號3
DOIs
出版狀態Published - 2017 三月 1

All Science Journal Classification (ASJC) codes

  • Physiology
  • Plant Science
  • Cell Biology

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