Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Oxidative stress transcriptome of japonica rice

ABSTRACT: Regulation of gene expression by reactive oxygen species (ROS) is an important component of abiotic stress signal transduction mechanisms. Previous genome-wide analysis of chilling-induced changes in gene expression suggested a potential role of H2O2 and other ROS as key signals in the induction of early response genes in japonica rice (cv. Nipponbare). Candidate regulators including bZIP-, Myb- or WRKY-types of transcription factors that were responsive to both chilling (10oC) and exogenous H2O2, and their probable target clusters (as1/ocs/TGA1-like, MybR-like element containing genes) were inferred by integrative analysis of qPCR expression profiles and ab initio promoter motif data. In an effort to define the composition and hierarchical organization of the ROS-mediated chilling response regulatory networks, we examined the effect of exogenous H2O2 (6 hours in 4mM H2O2 at 28oC and then 6 hours of recovery in water at 28oC) on the transcriptome of Nipponbare in a genome-wide scale and compared them with the chilling stress transcriptome. Results of this study were consistent with our earlier model that a ROSbZIP-as1/ocs/TGA1 regulatory module is a direct consequence of chilling-induced elevation of intracellular ROS during the initial 24 hours. Keywords: time course (response to exogenous H2O2) This experiment describes the analysis of the temporal changes in gene expression in response to exogenous H2O2 in Nipponbare rice. A total of 5 treatment regimes were examined (1, 3, and 6 hours at 4 mM H2O2 and then 3 and 6 hours of recovery in water after 6 hours of exposure to H2O2). The microarray platform used in this study was the 45K oligonucleotide microarray (www.ricearray.org) which comes in pairs of slides A and B (each containing about 50% of the total number of features). The data described in this series include all hybridizations with slide A and with slide B. All experiments were performed with two independent biological replicates (R1 and R2) for each time point.

ORGANISM(S): Oryza sativa

SUBMITTER: Kil-Young Yun

PROVIDER: E-GEOD-10062 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Transcriptional regulatory network triggered by oxidative signals configures the early response mechanisms of japonica rice to chilling stress.

Yun Kil-Young KY Park Myoung Ryoul MR Mohanty Bijayalaxmi B Herath Venura V Xu Fuyu F Mauleon Ramil R Wijaya Edward E Bajic Vladimir B VB Bruskiewich Richard R de Los Reyes Benildo G BG

BMC plant biology 20100125

<h4>Background</h4>The transcriptional regulatory network involved in low temperature response leading to acclimation has been established in Arabidopsis. In japonica rice, which can only withstand transient exposure to milder cold stress (10 degrees C), an oxidative-mediated network has been proposed to play a key role in configuring early responses and short-term defenses. The components, hierarchical organization and physiological consequences of this network were further dissected by a syste ...[more]

PMID: 20100339

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Project description:The central role of transcriptional regulation in integrating various low temperature response mechanisms has been established in Arabidopsis, where the CBF/DREB regulon plays a prominent role during acclimation. Rice is sensitive to chilling but many japonica cultivars can survive continuous exposure to as low as 10oC for up to 7 days during the most critical stage of seedling establishment better than most indica cultivars. The transcriptional regulatory networks that define this variation have not been studied in detail as cold acclimation has been scrutinized in Arabidopsis. Towards the comparison of the compositional complexity of low temperature response regulons of rice and Arabidopsis, we used the cultivar Nipponbare for genome-wide survey of regulatory clusters by integrative analysis of promoter architectures and temporal expression profiles during exposure to 10oC at narrow time intervals. Temporal profiles revealed major clusters of genes that were induced within the initial 24 hours. These clusters were further defined by common features of having either CRT/DRE-like elements, as1/ocs-like elements or both in their promoters. Genes containing as1/ocs-like elements with or without CRT/DRE, but not those containing only CRT/DRE-like elements were induced by exogenous H2O2 but not by ABA at ambient temperature, suggesting that they belong to a potential regulon (ROS-bZIP – as1/ocs module) that responds to elevated levels of reactive oxygen species (ROS) during the initial stages of stress. Parallel analysis of transcription factors during the initial 12 hours revealed candidate regulator(s) of this putative early response regulon. Cultivar-specific expression signatures of selected members of this regulatory cluster were also positively correlated with genotypic variation in chilling tolerance. We hypothesized that the ROS-bZIP – as1/ocs cluster has important roles in configuring the transcriptome of rice seedlings during the early stages of chilling stress and it appears to be independent of ABA and functions in parallel to the CBF/DREB regulon. Keywords: time course (response to low temperature) This experiment describes the analysis of the temporal changes in gene expression in response to chilling temperature in Nipponbare rice. A total of 10 stress time points, i.e., 0.5, 2, 4, 6, 12, 18, 24, 36, 48, and 96 hrs after exposure to 10C in a growth chamber and one recovery time point, i.e., 96 hrs at 10C and then 24 hrs (24R) at ambient or control temperature (29C), were profiled with reference to a corresponding control, which was exposed to ambient temperature (29C) for the same length of time under cold stress (each stress time point has a corresponding control sample). Control and cold stress samples were labeled with Cy5 and Cy3, respectively. No dye swap replicate was performed in this experiment. The microarray platform used in this study was the 45K oligonucleotide microarray (www.ricearray.org) which comes in pairs of slides A and B (each containing about 50% of the total number of features). The data described in this series include all hybridizations with slide A and with slide B. All experiments were performed with two independent biological replicates (R1 and R2) for each time point.

Dataset Information

Oxidative stress transcriptome of japonica rice

Publications

Transcriptional regulatory network triggered by oxidative signals configures the early response mechanisms of japonica rice to chilling stress.

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