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Microarray analysis of med14, med16, npr1, and wild type (Col-0) infected with the avirulent bacterial pathogen Pst DC3000/avrRpt2

ABSTRACT: The goal of the microarray experiment was to identify genes that are differentially expressed among the Arabidopsis mutant med14, med16, npr1, and wild type in response to infection of the avirulent bacterial pathogen Pst DC3000/avrRpt2. Results indicated that the induction of a large group of defense genes was suppressed in the med14 mutant compared with both med16 and the wild type.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE45214 | GEO | 2013/05/18

SECONDARY ACCESSION(S): PRJNA193215

REPOSITORIES: GEO

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Microarray analysis of med14, med16, npr1, and wild type (Col-0) infected with the avirulent bacterial pathogen Pst DC3000/avrRpt2

Project description:The goal of the microarray experiment was to identify genes that are differentially expressed among the Arabidopsis mutant med14, med16, npr1, and wild type in response to infection of the avirulent bacterial pathogen Pst DC3000/avrRpt2. Results indicated that the induction of a large group of defense genes was suppressed in the med14 mutant compared with both med16 and the wild type. Three biological replicates with leaves from 8 plants per sample were collected at 0 and 4 hours after inoculation with the avirulent bacterial pathogen Pst DC3000/avrRpt2. After extraction, RNA concentration was determined on a NanoDrop Spectrophotometer (Thermofisher Scientific, Waltham, MA) and sample quality was assessed using the 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). Each replicate was used as one sample for microarray analysis.

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Microarray analysis of med14 and wild type (Col-0) infected with the avirulent bacterial pathogen Pst DC3000/avrRpt2

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Microarray analysis of med14 and wild type (Col-0) infected with the avirulent bacterial pathogen Pst DC3000/avrRpt2

Project description:The goal of the microarray experiment was to determine the induction kinetics of transcriptome changes and to identify differentially expressed genes in the Arabidopsis mutant med14 and wild type in response to infection of the avirulent bacterial pathogen Pst DC3000/avrRpt2. Results indicated that med14 exhibited slower kinetcis of transcriptional changes than the wild type after Pst DC3000/avrRpt2 infection, and the induction of a large group of defense genes was suppressed in the med14 mutant. Three biological replicates with leaves from 8 plants per sample were collected at 0, 4, 8, and 12 hours after inoculation with the avirulent bacterial pathogen Pst DC3000/avrRpt2. After extraction, RNA concentration was determined on a NanoDrop Spectrophotometer (Thermofisher Scientific, Waltham, MA) and sample quality was assessed using the 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). Each replicate was used as one sample for microarray analysis.

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Microarray analysis of At-med16-1 and wild type (Col-0) infected with the avirulent bacterial pathogen Pst DC3000/avrRpt2

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Microarray analysis of At-med16-1 and wild type (Col-0) infected with the avirulent bacterial pathogen Pst DC3000/avrRpt2

Project description:The goal of the microarray experiment was to identify defense genes that were differentially expressed in the Arabidopsis mutant At-med16-1 and wild type in response to infection of the avirulent bacterial pathogen Pst DC3000/avrRpt2. Results indicated that, compared with the wild type, several positive regulators of SAR (systemic acquired resistance) were downregulated and a group of SAR negative regulators were upregulated in At-med16-1. Three biological replicates with leaves from 8 plants per sample were collected at 0, 4, 8, and 24 hours after inoculation with the avirulent bacterial pathogen Pst DC3000/avrRpt2. After extraction, RNA concentration was determined on a NanoDrop Spectrophotometer (Thermofisher Scientific, Waltham, MA) and sample quality was assessed using the 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). Equal amount of RNA from the 3 biological replicates were pooled as one sample for microarray analysis.

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Connection of core and and tail Mediator modules restrains transcription from TFIID-dependent promoters [ChEC-seq Med16-AID]

Project description:The Mediator coactivator complex is divided into four modules: head, middle, tail, and kinase. Deletion of the architectural subunit Med16 separates core Mediator (cMed), comprising the head, middle, and scaffold (Med14), from the tail. However, the direct global effects of tail/cMed disconnection are unclear. We find that rapid depletion of Med16 downregulates genes that require the SAGA complex for full expression, consistent with their reported tail dependence, but also moderately overactivates TFIID-dependent genes in a manner partly dependent on the separated tail, which remains associated with upstream activating sequences. Suppression of TBP dynamics via removal of the Mot1 ATPase partially restores normal transcriptional activity to Med16-depleted cells, suggesting that cMed/tail separation results in an imbalance in the levels PIC formation at SAGA-requiring and TFIID-dependent genes. We suggest that the preferential regulation of SAGA-requiring genes by tailed Mediator helps maintain a proper balance of transcription between these genes and those more dependent on TFIID.

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