Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Expression profiling of small RNAs in control and H2O2-treated rice seedlings

ABSTRACT: We aimed to identify putative H2O2-regulated miRNAs expressed in rice seedlings under oxidative stress by using a deep sequencing approach developed by Solexa (Illumina). Two small RNA libraries were constructed from H2O2-treated and control rice seedlings, and more than five million small RNA sequence reads were generated for each library. We identified seven H2O2-responsive miRNA families via expression profiling of the miRNAs based on a comparative miRNAomic analysis in combination with experimental validation. Furthermore, 32 miRNAs, 17 from known miRNA loci and 15 from novel miRNA loci, were also newly identified from the sequencing data. To the best of our knowledge, this is the first report of a systematic investigation of H2O2-regulated miRNAs and their targets in plants. Examination of 2 different small RNA expression profilings in the control and H2O2 treated rice samples.

ORGANISM(S): Oryza sativa

SUBMITTER: Tian Li

PROVIDER: E-GEOD-23217 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Identification and analysis of seven H₂O₂-responsive miRNAs and 32 new miRNAs in the seedlings of rice (Oryza sativa L. ssp. indica).

Li Tian T Li Hui H Zhang Yun-Xiao YX Liu Jin-Yuan JY

Nucleic acids research 20101127 7

Plant microRNAs (miRNAs) have been shown to play critical roles in regulating gene expression at the post-transcriptional level. In this study, we employed high throughput sequencing combined with computational analysis to survey miRNAomes from the seedlings of rice under normal conditions and treatments of H(2)O(2) that result in oxidative stress. Comparison of the miRNAomes and subsequent northern blot analysis identified seven miRNA families differentially expressed under H(2)O(2) stress. Pre ...[more]

PMID: 21113019

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Project description: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.

Dataset Information

Expression profiling of small RNAs in control and H2O2-treated rice seedlings

Publications

Identification and analysis of seven H₂O₂-responsive miRNAs and 32 new miRNAs in the seedlings of rice (Oryza sativa L. ssp. indica).

Similar Datasets

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