A Local Regulatory Network Around Three NAC Transcription Factors in Stress Responses and Senescence in Arabidopsis leaves
Ontology highlight
ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
SUBMITTER: Jonathan Moore
PROVIDER: E-GEOD-46318 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Publications
A local regulatory network around three NAC transcription factors in stress responses and senescence in Arabidopsis leaves.
Hickman Richard R Hill Claire C Penfold Christopher A CA Breeze Emily E Bowden Laura L Moore Jonathan D JD Zhang Peijun P Jackson Alison A Cooke Emma E Bewicke-Copley Findlay F Mead Andrew A Beynon Jim J Wild David L DL Denby Katherine J KJ Ott Sascha S Buchanan-Wollaston Vicky V
The Plant journal : for cell and molecular biology 20130511 1
A model is presented describing the gene regulatory network surrounding three similar NAC transcription factors that have roles in Arabidopsis leaf senescence and stress responses. 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 modelling using gene expression time course data has been applied to predict the regulatory network upstrea ...[more]
Similar Datasets
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
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 10μl 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
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
Project description:A novel experimental design strategy (A Mead et al, in preparation), based on the principle of the M-bM-^@M-^\loop designM-bM-^@M-^], was developed to enable efficient extraction of information about key sample comparisons using a two-colour hybridisation experimental system. With 192 distinct samples (four biological replicates at each of 24 time points in mock and treated conditions) to be compared, the experimental design included 288 two-colour microarray slides, allowing four technical replicates of each sample to be observed. One third of the slides were devoted to assessment of changes in gene expression between time points, using a simple loop design to link samples from time points across the 24 sampled times, directly comparing samples collected on adjacent sampling times (i.e. 2 hrs post-infection with 4 hrs post-infection, 4 hrs post-infection with 6 hrs post-infection, etc.). With the remaining slides, four separate loops were constructed comparing treatments, biological replicates and samplling times. infected vs. mock, 24 time points, randomized loop, 576 Imagene files
2012-10-02 | E-GEOD-29642 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the following subset Series: GSE29642: Arabidopsis defense against Botrytis cinerea: chronology and regulation deciphered by high-resolution temporal transcriptomic analysis (time series) GSE39597: Arabidopsis defense against Botrytis cinerea: chronology and regulation deciphered by high-resolution temporal transcriptomic analysis (tga3-2 knockout data) Refer to individual Series
2012-10-03 | E-GEOD-39598 | biostudies-arrayexpress
Project description:Leaf senescence is an essential developmental process that involves altered regulation of thousands of genes and changes in many metabolic and signaling pathways resulting in massive physiological and structural changes in the leaf. The regulation of senescence is complex and although several senescence regulatory genes have been identified and characterized there is little information on how these individual regulators function globally in the control of the process. In this paper we use microarray analysis to obtain a high-resolution time course profile of gene expression during development of a single leaf over a three week period from just before full expansion to senescence. The multiple time points enable the use of highly informative clustering tools to reveal distinct time points at which signaling and metabolic pathways change during senescence. Analysis of motif enrichment in co-regulated gene clusters identifies clear groups of transcription factors active at different stages of leaf development and senescence. A novel experimental design strategy (A Mead et al, in preparation), based on the principle of the “loop design”, was developed to enable efficient extraction of information about key sample comparisons using a two-colour hybridisation experimental system. With 88 distinct samples (four biological replicates at each of 22 time points) to be compared, the experimental design included 176 two-colour microarray slides, allowing four technical replicates of each sample to be observed. Half of the slides were devoted to assessment of changes in gene expression between time points, using a simple loop design to link 11 samples from either the 7h time points or the 14h time points across the 11 sampling days, directly comparing samples collected on adjacent sampling days (i.e. 19 DAS with 21 DAS, 27 DAS with 29 DAS, etc.), and directly comparing the samples collected at 39 DAS with those collected at 19 DAS. Four separate loops were constructed for the 7h time points and for the 14h time points, using the arbitrary biological replicate labelling to identify the samples to be included in each loop. The remaining slides provided assessment of differences between the 7h and 14h samples and between the arbitrarily labelled biological replicates, with some further assessment of changes between sampling days. All direct comparisons (pairs of samples hybridised together on a slide) were between 7h and 14h samples collected on adjacent sampling days (i.e. 19 DAS with 21 DAS, etc.), including comparisons between samples collected at 39 DAS and at 19 DAS, and different arbitrarily labelled biological replicates. These 88 comparisons formed a single loop connecting all 88 treatments, therefore ensuring that the design was fully connected (allowing each sample to be compared with every other sample).
2011-03-24 | E-GEOD-22982 | biostudies-arrayexpress
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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2020-09-15 | PXD018814 | Pride
Project description:Plants as multi cellular organisms are composed of various specialized cell types. Most of these cell types are symplasmically connected via plasmodesmata (PD) allowing exchange of nutrients and signal molecules. To date, the molecular composition of PD is not well understood. A comprehensive and comparative proteomic approach was followed to identify proteins providing new insights into the composition of these important regulatory structures.
2017-09-05 | PXD006880 | Pride