Similar Datasets
Project description:Time-course transcriptional profiling of senescing barley leaves. In this model, the senescence process was induced by continued incubation of the seedlings in darkness. Plant samples for the expression analysis were collected before senescence induction (Day 0) and after 3,7 and 10 days of incubation in the dark. The goal was to find the genes differentially expressed during the senescence process . Additionally, a list of the genes with the invariant expression was generated as a resource for selecting references suitable for qPCR or ddPCR experiments. Time-course experiment, two-color, common reference design. All of the data were obtained from material collected in three independent, time-separated leaf senescing experiments (biological replicates). In each replicate, samples from senescing leaves (3 Days, 7 Days, 10 Days) were compared to samples collected before the senescence induction (Day 0). 3 biological replicates.Cy5-labeled samples of interest (Day 0, Day 3, Day 7 and Day 10 from each biological replicate) were each hybridized against a Cy3-labeled common reference (RNA pool of all samples) on a total of 12 microarrays.
2014-10-22 | E-GEOD-62539 | biostudies-arrayexpress
Project description:Leaf senescence can be triggered by jasmonic acid (JA) and darkness. There are scattered reports about JA and dark-induced senescence, respectively. While the precise regulatory mechanisms that integrate these two factors to initiate and regulate leaf senescence have not been identified. Here, we report a transcriptional regulating module centered on novel WRKY transcription factor that is responsible for both JA and dark-induced leaf senescence in tomato. The expression levels of SlWRKY37 together with the master transcription factor in JA signaling SlMYC2 could be significantly induced by both MeJA and dark treatments. SlMYC2 directly binds to the promoter of SlWRKY37 to active its expression. Knock out of SlWRKY37 inhibited JA and dark-induced leaf senescence. Transcriptome analysis revealed 1312 differentially expressed genes between slwrky37-CR and SlWRKY37-OE, including genes involved in JA synthesis as well as several senescence-associated genes (SAGs). We characterized SlWRKY53 and SlSGR1 as direct transcriptional targets of SlWRKY37 to regulate leaf senescence. Moreover, SlWRKY37 interacts with SlVQ7 protein in vivo and the interaction enhances its binding ability to the promoters and transcriptional activation to downstream target genes. In addition, SlWRKY37 is phosphorylated at the post-translational level. Phosphorylation of SlWRKY37 is essential for its protein interaction and transcriptional activation, indicating phosphorylation modification has a great effect on the function of SlWRKY37 protein. Our study reveals the physiological and molecular functions of SlWRKY37 in leaf senescence and offered a target gene to retard leaf yellowing by reducing the sensitivity to internal and external senescence signal such as JA and darkness.
2022-06-01 | GSE186072 | GEO
Project description:Time-course transcriptional profiling of senescing barley leaves. In this model, the senescence process was induced by continued incubation of the seedlings in darkness. Plant samples for the expression analysis were collected before senescence induction (Day 0) and after 3,7 and 10 days of incubation in the dark. The goal was to find the genes differentially expressed during the senescence process . Additionally, a list of the genes with the invariant expression was generated as a resource for selecting references suitable for qPCR or ddPCR experiments.
2014-10-22 | GSE62539 | GEO
Project description:Transcriptional profiling of Arabidopsis dark-induced senescence comparing wild type (Col-0) with pif quadruple (pif1/3/4/5) mutant. After synchronized germination, the plants were grown under continuous white light for 7 days and transferred to darkness for 2 days to induce senescence. Goal was to determine the effect of PIFs on transcriptomic regulation during dark-induced senescence.
2014-08-04 | GSE52646 | GEO
Project description:To find the miRNAs that may be involved in dark-induced leaf senescence, we identified miRNAs by microarray platform using Arabidopsis thaliana leaves from both whole darkened plants (DPs) and individually darkened leaves (IDLs). Control, IDLs and DPs were treated for 2, 4 or 6 d in the same climate chambers (16 h light/8 h dark, 250 mmol m-2 s-1).
2016-09-19 | GSE74376 | GEO
Project description:Transcriptional profiling of Arabidopsis dark-induced senescence comparing wild type (Col-0) with pif quadruple (pif1/3/4/5) mutant. After synchronized germination, the plants were grown under continuous white light for 7 days and transferred to darkness for 2 days to induce senescence. Goal was to determine the effect of PIFs on transcriptomic regulation during dark-induced senescence. Two-condition experiment, wild type vs. pif quadruple mutant. Biological replicates: 3 wild type replicates, 3 mutant replicates.
2014-08-04 | E-GEOD-52646 | biostudies-arrayexpress
Project description:Gene expression was measured in leaves from dark treated tobacco plants to investigate the changes associated with dark induced senescence.
2011-05-01 | E-MTAB-602 | 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 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:The aim of this experiment was to decipher a transcriptional regulatory code of Arabidopsis Auxin Response Factor 2 (ARF2) and understand the molecular basis of ARF2’s role as a promoter of dark-induced senescence. A combination of computational tools and yeast one-hybrid experiments identified potential direct transcriptional regulators of ARF2 belonging to several TF families including AP2/ERFs and AREB/ABF/ABI5s. Using ARF2 promoter mutants in transcriptional activation and Y1H experiments, the binding sites of these TFs in the ARF2 promoter were identified. AP2/ERFs including ERF1, ERF15 and ORA59 transactivate the ARF2 promoter in Arabidopsis mesophyll protoplasts and this transactivation is positively regulated by ABA. Crucially, the positive effect of ABA on ERF1 transactivation of ARF2 relies on the functional ABRE motif in the ARF2 promoter and the presence of AREB/ABF/ABI5s (ABF3 and ABF4) suggesting the existence of combinatorial regulation of ARF2 by these direct regulators. ABF3 and ABF4 were unable to activate the ARF2 promoter on their own indicating the necessity of ERF1 as a coupling TF for AREB/ABF/ABI5-driven regulation of ARF2. We also show that MED25 (a subunit of the Mediator complex) is required for proper transcriptional regulation of ARF2 during senescence. med25 plants show decreased ARF2 mRNA levels during natural senescence and, similarly to arf2-6 mutants, exhibit a delayed dark-induced senescence phenotype. We show that MED25 is important for ERF1-, ERF15- and ORA59-dependent transactivation of ARF2 in Arabidopsis protoplasts and finally idenitfy genes differentially expressed in arf2-6 mutants compared to wildtype during dark-induced senescence. Hence, we elucidate a regulatory network around ARF2 identifying combinatorial transcriptional regulation of this gene during senescence as well as likely downstream targets. The combinatorial regulation, comprised of AP2/ERFs and AREB/ABF/ABI5s TFs, enables integration of at least two key hormone signaling pathways to drive expression of a key senescence regulator.
2022-09-30 | GSE150569 | GEO
Project description:Leaf senescence, the last step of leaf development which is important for plant’s fitness, proceeds with age but is modulated by various environmental stresses and hormones. Salt stress is one of the well-known environmental stresses that accelerate leaf senescence. However, the molecular mechanisms how the signal of salt stress is integrated into leaf senescence programs are still elusive. In this study, we characterized the function of an Arabidopsis APETALA 2/ETHYLENE RESPONSIVE FACTOR (AP2/ERF) family transcription factor, ERF34, in salt stress-induced leaf senescence. ERF34 was differentially expressed under leaf senescence-inducing conditions including age, dark, and high salt. ERF34 negatively regulated salt stress-induced leaf senescence as well as promoted salt stress tolerance at diverse developmental stages. Analysis of genome-wide targets of ERF34 revealed that the overexpression of ERF34 could alter salt-responsive gene expression. Moreover, ERF34 directly bound to the promoters of EARLY RESPONSIVE TO DEHYDRATION 10 and RESPONSE TO DESICCATION 29A and activated their expression. Our findings imply that ERF34 is a key regulator in the convergence of salt stress response with the regulatory programs of leaf senescence and is a potential candidate for crop improvement, particularly by enhancing salt stress tolerance.
2024-07-01 | GSE180096 | GEO