Unknown,Transcriptomics,Genomics,Proteomics

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Transcription profiling of Arabidopsis response to Response to Botrytis cinerea infection - AtGenExpress pathogen series

ABSTRACT: AtGenExpress: A multinational coordinated effort to uncover the transcriptome of the multicellular model organism Arabidopsis thaliana; 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. Responses to B. cinerea infection were assayed in wild-type Col-0 plants at 18 and 48 hours after inoculation of adult leaves. Leaves were inoculated by placing 4 5-ul drops of a 5x10e5 spore solution on each leaf. Control leaves were spotted with droplets of 24g L-1 potato dextrose broth medium. Experimenter name = Carine Denoux , Fred Ausubel , Julia Dewdney , Simone Ferrari; Experimenter institute = AtGenExpress Experiment Overall Design: 12 samples were used in this experiment

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Nottingham Arabidopsis Stock Centre (NASC)

PROVIDER: E-GEOD-5684 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Transcriptional reprogramming forms a major part of a plant's response to pathogen infection. Many individual components and pathways operating during plant defense have been identified but our knowledge of how these different components interact is still rudimentary. We have generated a high-resolution time series of gene expression profiles from a single Arabidopsis leaf during infection by the necrotrophic fungal pathogen, Botrytis cinerea. Approximately one-third of the Arabidopsis genome is differentially expressed during the first 48 hours after infection, with the majority of gene expression changes occurring before significant lesion development. We have used computational tools to obtain a detailed chronology of the defense response against B. cinerea, highlighting the times at which signaling and metabolic processes change, and identify transcription factor families operating at different times after infection. Motif enrichment and network inference predicted regulatory interactions and testing of one such prediction identified a novel role for TGA3 in defense against necrotrophic pathogens. These data provide an unprecedented level of detail about transcriptional change during a defense response and are suited to systems biology analyses to generate predictive models of the gene regulatory networks underlying the Arabidopsis response to B. cinerea. Samples were compared at three time points: 16, 24 and 32 hours post infection. Time points were chosen based on the expression profile of TGA3 in the high-resolution time series also presented in this paper. Samples were collected for three different conditions: tga3-2 mock inoculated, tga3-2 infected and Col-0 infected. Four individual leaves (biological replicates) from separate plants were collected for each treatment-time point totalling 36 samples. The four biological replicates for each treatment-time point were pooled. At each time point, the expression of the 4 pooled replicates was compared between tga3-2 mock inoculated vs. tga3-2 infected and tga3-2 infected vs. Col-0 infected using four technical replicates for each comparison which included balanced dye swaps.

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Transcription profiling of Arabidopsis response to Response to Botrytis cinerea infection - AtGenExpress pathogen series

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