Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Genome-wide analysis of siRNA accumulation in Arabidopsis treated with bacteria

ABSTRACT: To identify endogenous siRNAs in response to bacterial pathogen at a whole genome level, we performed small RNA profiling on Pseudomonas syringae-challenged Arabidopsis and obtained more than 24.6 million (M) reads with more than 3.8 M unique small RNAs that perfectly matched Arabidopsis genome. We found some new miRNAs and some miRNA induced by pathogen infection. We also identified more than 20K unique siRNAs from the NAT mRNAs and 22K siRNAs from the introns or intron-exon junction of the NATs. Sequencing of small RNAs from Arabidopsis infected by control and 3 bacterias in 6h and 14h.

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Weixiong Zhang

PROVIDER: E-GEOD-19694 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Multiple distinct small RNAs originate from the same microRNA precursors.

Zhang Weixiong W Gao Shang S Zhou Xuefeng X Xia Jing J Chellappan Padmanabhan P Zhou Xiang X Zhang Xiaoming X Jin Hailing H

Genome biology 20100809 8

<h4>Background</h4>MicroRNAs (miRNAs), which originate from precursor transcripts with stem-loop structures, are essential gene expression regulators in eukaryotes.<h4>Results</h4>We report 19 miRNA precursors in Arabidopsis that can yield multiple distinct miRNA-like RNAs in addition to miRNAs and miRNA*s. These miRNA precursor-derived miRNA-like RNAs are often arranged in phase and form duplexes with an approximately two-nucleotide 3'-end overhang. Their production depends on the same biogenes ...[more]

PMID: 20696037

Publication: 1/3

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Project description:Plants have evolved a two-layered immune system that mainly includes pattern-triggered immunity (PTI) and effector-triggered immunity (ETI) against pathogen attack. PTI and ETI signaling are functionally linked, but also distinct due to specific perceived ligands and activation modes. Unraveling how PTI and ETI coordinate the immune responses against pathogens is crucial for understanding the regulatory mechanisms in plant immunity. To better understand the protein profiling and phosphorylation events during PTI and ETI, we employed integrated whole proteome and phosphoproteome analyses in the tomato-Pst pathosystem with different Pst DC3000 mutants that allow dissection of different layers of immune responses. A total of 225 proteins and 79 phosphopeptides were differentially regulated in tomato leaves during immune responses. Our proteomics results indicate that some overlapping immune responses are triggered by both PTI and ETI-inducing treatment, and ETI response is more robust than PTI response for most proteins. The change patterns of protein abundance and phosphorylation revealed some key regulators involved in Ca2+ signaling, mitogen-activated protein kinase cascades, and reversible protein phosphorylation, ROS and redox homeostasis, direct defense, transcription machinery and protein turnover, cell wall remodeling, hormone biosynthesis, as well as immune molecule accumulation, are modulated during PTI and/or ETI, suggesting their common or specific roles in plant immune responses. However, NAC domain protein and lipid particle serine esterase, two PTI-specific genes from previous transcriptomic work, have not been detected as differentially regulated in our proteomic analysis, and they were proved to be not PTI-specific inducible and therefore cannot be used as PTI-reporters through “overlapping circle” pattern assay. These results provide insights into the fine-tuned regulatory mechanisms between PTI and ETI in-Pst pathosystem, which will springboard further investigations into the sophisticated mechanisms in plant immunity.

Project description:AtGenExpress: A multinational coordinated effort to uncover the transcriptome of the multicellular model organism Arabidopsis thaliana (Hybridisations done at NASC); The activity of genes and their encoded products can be regulated in several ways, but transcription is the primary level, since all other modes of regulation (RNA splicing, RNA and protein stability, etc.) are dependent on a gene being transcribed in the first place. The importance of transcriptional regulation has been underscored by the recent flood of global expression analyses, which have confirmed that transcriptional co-regulation of genes that act together is the norm, not the exception. Moreover, many studies suggest that evolutionary change is driven in large part by modifications of transcriptional programs. An essential first step toward deciphering the transcriptional code is to determine the expression pattern of all genes. With this goal in mind, an international effort to develop a gene expression atlas of Arabidopsis has been underway since fall 2003. This project, dubbed AtGenExpress, is funded by the DFG, and will provide the Arabidopsis community with access to a large set of Affymetrix microarray data. As part of this collaboration, we have generated expression data from 80 biologicaly different samples in triplicate. Series 2: Base line experiment for pathogen infection. Growth and infection conditions: Seeds will be stratified for 3 days at 4Â°C and sown on soil. Plants are grown at 22Â°C under a 8/16 hour light/dark regime in Percival growth chambers. All pathogen treatments will be performed on leaves of 5-weeks old plants. Bacterial infiltrations will be performed with 10-8 cfu/ml in 10 mM MgCl2. 5x105 spores of Phytophthora infestans in water will be applied to leaf surfaces. LPS (100 Âµg/ml), HrpZ (1 ÂµM), NPP1 (2 ÂµM) or flagellin (1 ÂµM flg22) will be applied in water. Experiments should be performed in triplicate at the time points indicated below. Experimenter name = Frederic Brunner , Thorsten NÃ¼rnberger; Experimenter institute = AtGenExpress Experiment Overall Design: 42 samples were used in this experiment

Dataset Information

Genome-wide analysis of siRNA accumulation in Arabidopsis treated with bacteria

Publications

Multiple distinct small RNAs originate from the same microRNA precursors.

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