title: Common Stress Transcriptome Analysis Reveals Functional and Genomic Architecture Differences Between Early and Delayed Response Genes.
abstract: 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.
authors.affiliation: Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan.
authors.forename: Chung-Wen
authors.initials: CW
authors.lastname: Lin
authors.affiliation: Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan.
authors.forename: Li-Yao
authors.initials: LY
authors.lastname: Huang
authors.affiliation: Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan.
authors.forename: Chao-Li
authors.initials: CL
authors.lastname: Huang
authors.affiliation: Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan.
authors.forename: Yong-Chuan
authors.initials: YC
authors.lastname: Wang
authors.affiliation: Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan, Taiwan.
authors.forename: Pei-Hsuan
authors.initials: PH
authors.lastname: Lai
authors.affiliation: Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan.
authors.forename: Hao-Ven
authors.initials: HV
authors.lastname: Wang
authors.affiliation: Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan, Taiwan.
authors.forename: Wen-Chi
authors.initials: WC
authors.lastname: Chang
authors.affiliation: Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan.
authors.forename: Tzen-Yuh
authors.initials: TY
authors.lastname: Chiang
authors.affiliation: Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan.|Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan, Taiwan.
authors.forename: Hao-Jen
authors.initials: HJ
authors.lastname: Huang
mesh_terms: D002857:Chromium / Q000633:toxicity; D003373:Coumaric Acids / Q000633:toxicity; D020869:Gene Expression Profiling / Q000379:methods*; D018506:Gene Expression Regulation, Plant / Q000187:drug effects / Q000235:genetics; D008628:Mercury / Q000633:toxicity; D012275:Oryza / Q000187:drug effects / Q000235:genetics; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D013312:Stress, Physiological
chemical_list: D003373:Coumaric Acids; D010940:Plant Proteins; D002857:Chromium; C004999:ferulic acid; D008628:Mercury
keywords: Gene structure; Network component analysis; Rapid evolution; Rice; Temporal dynamics of stress response