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A Local Regulatory Network Around Three NAC Transcription Factors in Stress Responses and Senescence in Arabidopsis leaves

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE46318 | GEO | 2013/04/23

SECONDARY ACCESSION(S): PRJNA198725

REPOSITORIES: GEO

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A local regulatory network around three NAC transcription factors in stress responses and senescence in Arabidopsis leaves.

Project description: Not available

| S-EPMC3781708 | biostudies-literature

A Local Regulatory Network Around Three NAC Transcription Factors in Stress Responses and Senescence in Arabidopsis leaves

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2013-04-23 | E-GEOD-46318 | biostudies-arrayexpress

A Local Regulatory Network Around Three NAC Transcription Factors in Stress Responses and Senescence in Arabidopsis leaves (Dark Induced Senescence).

Project description:A network model has been generated that describes the immediate gene expression cascade surrounding three similar but distinct NAC transcription factors that have roles to play in leaf senescence and in many stress responses in Arabidopsis. ANAC019, ANAC055 and ANAC072 belong to the same clade of NAC domain genes and have overlapping expression patterns. A combination of promoter DNA/protein interactions identified using yeast 1 hybrid analysis and modeling using gene expression time course data has been used to predict the regulatory network upstream of these genes. Similarities and divergence in regulation during a variety of stress responses are predicted by different combinations of upstream transcription factors binding and also by the modeling. Mutant analysis with potential upstream genes was used to test and confirm some of the predicted interactions.. Gene expression measurements in mutants of ANAC019 and ANAC055 at different times during leaf senescence have shown a distinctly different role for each of these genes. To assess mutant response to Dark Induced Senescence (DIS), leaf5 from transplanted rosettes, subjected to dark conditions, from Col-0, myb2 (genotype IM24) and myb108 (genotype BOS1) knockout plants, were photographically assessed for red/green ratio. When the average ratio for Col-0 samples was >0.8, leaf 5 for Col-0, myb2 and myb108 lines was harvested (4 biological replicates). The same sampling procedure was then performed on consecutive days to sample as senescence progressed. Analysis of expression differences between Col-0 and myb2 and Col-0 and myb108 under each condition, using dye swaps, was performed using the R Bioconductor package limmaGUI (Wettenhall and Smyth, 2004).

2013-04-23 | E-GEOD-45595 | biostudies-arrayexpress

A Local Regulatory Network Around Three NAC Transcription Factors in Stress Responses and Senescence in Arabidopsis leaves (Dark Induced Senescence).

2013-04-23 | GSE45595 | GEO

A Local Regulatory Network Around Three NAC Transcription Factors in Stress Responses and Senescence in Arabidopsis leaves (Botrytis cinerea infection).

2013-04-23 | GSE45594 | GEO

A Local Regulatory Network Around Three NAC Transcription Factors in Stress Responses and Senescence in Arabidopsis leaves (Botrytis cinerea infection).

Project description:A network model has been generated that describes the immediate gene expression cascade surrounding three similar but distinct NAC transcription factors that have roles to play in leaf senescence and in many stress responses in Arabidopsis. ANAC019, ANAC055 and ANAC072 belong to the same clade of NAC domain genes and have overlapping expression patterns. A combination of promoter DNA/protein interactions identified using yeast 1 hybrid analysis and modeling using gene expression time course data has been used to predict the regulatory network upstream of these genes. Similarities and divergence in regulation during a variety of stress responses are predicted by different combinations of upstream transcription factors binding and also by the modeling. Mutant analysis with potential upstream genes was used to test and confirm some of the predicted interactions.. Gene expression measurements in mutants of ANAC019 and ANAC055 at different times during leaf senescence have shown a distinctly different role for each of these genes. To assess mutant response to Botrytis cinerea infection, Col-0, myb2 and myb108 leaves were inoculated with 4-6 (depending on leaf size) evenly spaced 10Î¼l droplets of B. cinerea spores. Infected leaves were harvested to provide 4 biological replicates. Samples for the comparison between myb108 and Col-0 were harvested at 26 and 30 hpi. Samples for the comparison between myb2 knockout line and Col-0 or myb2 knockout line and Col-0 were harvested at 26 and 30 hpi or 24 and 30 hpi respectively. Analysis of expression differences between Col-0 and myb2 and Col-0 and myb108 under each condition, using dye swaps, was performed using the R Bioconductor package limmaGUI (Wettenhall and Smyth, 2004).

2013-04-23 | E-GEOD-45594 | biostudies-arrayexpress

A Local Regulatory Network Around Three NAC Transcription Factors in Stress Responses and Senescence in Arabidopsis leaves (expression between lines at timepoints).

2013-04-23 | GSE45183 | GEO

A Local Regulatory Network Around Three NAC Transcription Factors in Stress Responses and Senescence in Arabidopsis leaves (expression between lines at timepoints).

Project description:A network model has been generated that describes the immediate gene expression cascade surrounding three similar but distinct NAC transcription factors that have roles to play in leaf senescence and in many stress responses in Arabidopsis. ANAC019, ANAC055 and ANAC072 belong to the same clade of NAC domain genes and have overlapping expression patterns. A combination of promoter DNA/protein interactions identified using yeast 1 hybrid analysis and modeling using gene expression time course data has been used to predict the regulatory network upstream of these genes. Similarities and divergence in regulation during a variety of stress responses are predicted by different combinations of upstream transcription factors binding and also by the modeling. Mutant analysis with potential upstream genes was used to test and confirm some of the predicted interactions.. Gene expression measurements in mutants of ANAC019 and ANAC055 at different times during leaf senescence have shown a distinctly different role for each of these genes. Leaf 7 from the anac019 (genotype 9C11) and anac055 (genotype IM4) mutants and their WT controls, Col-5 and Col-0 respectively, was tagged with cotton 18 days after sowing (DAS) and harvested from five randomly selected plants (biological replicates), 8 h into the light period, at 23, 29, 31, 33 and 35 DAS (full senescence). Variance in expression between lines at timepoints was analysed using a local adaptation of the MAANOVA package as previously described (Breeze et al., Plant Cell 2011 Mar;23(3):873-94. PMID: 21447789) using a loop design including dye swaps. Genotype DM (double mutant cross between IM4 and 9C11) was also included in the experiment, and was part of the loop design. Results for DM are included here in so far as they played a role in the ANOVA definition of values, but are not discussed in the paper.

2013-04-23 | E-GEOD-45183 | biostudies-arrayexpress