ABA-responsive gene expression under shade
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA559086 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Microarray analysis to investigate the global gene expression patterns in response to ABA under different light quality backgrounds
2020-12-01 | GSE135489 | GEO
Project description:The goal of this study is to obtain genome-wide shade-responsive genes in adult plant. We grew plants under long-day condition with high R/FR ratio (simulated "sun" condition) for two weeks. Plants were treated with shade starting at ZT 4 or left in the sun. We prepared two replicates of each sample at 1 hour and 4 hours after sun and shade treatment and five plants were pooled for each replicate. Cotyledons, hypocotyls, and roots were removed from the samples, leaving leaves and apical tissue.
2015-03-18 | GSE66967 | GEO
Project description:Accessible chromatin regions host DNA regulatory motives and are highly accessible to the transcription factors and transcriptional machinery. In Arabidopsis, responses to light are heavily regulated at the transcriptional level. Shade, for example, can limit photosynthesis and is rapidly perceived by phytochromes as a reduction of red to far-red light ratio. Under shade, phytochromes inactivate and allow PHYTOCHROME INTERACTING FACTORs (PIFs) to promote a wide scale genome reprogramming. A strong and fast initial regulation of shade responsive genes is followed by an attenuation of this response under prolonged shade. We wanted to determine if transcriptional response pattern to shade depends on chromatin accessibility. For this we used ATAC-seq to profile the chromatin of seedlings exposed to short (1h) and long (25h) simulated shade. Transcription pattern of most acute shade responsive genes correlates with the rapid increase in PIF levels/activity at 1h, and its decrease at 25h of shade exposure. For a set of acute responding genes, PIFs also modulate chromatin accessibility at their binding sites in response to shade. Our results suggest that permanent state of open chromatin conformation allows PIFs to easily access and recognize their binding motifs, rapidly initiating a burst in gene expression triggered by shade. This transcriptional response primarily depends on a transient increase in stability of PIFs and gene occupancy and is followed by a moderate change of chromatin accessibility.
2025-11-06 | GSE283129 | GEO
Project description:Accessible chromatin regions host DNA regulatory motives and are highly accessible to the transcription factors and transcriptional machinery. In Arabidopsis, responses to light are heavily regulated at the transcriptional level. Shade, for example, can limit photosynthesis and is rapidly perceived by phytochromes as a reduction of red to far-red light ratio. Under shade, phytochromes inactivate and allow PHYTOCHROME INTERACTING FACTORs (PIFs) to promote a wide scale genome reprogramming. A strong and fast initial regulation of shade responsive genes is followed by an attenuation of this response under prolonged shade. We wanted to determine if transcriptional response pattern to shade depends on chromatin accessibility. For this we used ATAC-seq to profile the chromatin of seedlings exposed to short (1h) and long (25h) simulated shade. Transcription pattern of most acute shade responsive genes correlates with the rapid increase in PIF levels/activity at 1h, and its decrease at 25h of shade exposure. For a set of acute responding genes, PIFs also modulate chromatin accessibility at their binding sites in response to shade. Our results suggest that permanent state of open chromatin conformation allows PIFs to easily access and recognize their binding motifs, rapidly initiating a burst in gene expression triggered by shade. This transcriptional response primarily depends on a transient increase in stability of PIFs and gene occupancy and is followed by a moderate change of chromatin accessibility.
2025-11-06 | GSE283133 | GEO
Project description:To compare the genome-wide transcriptional effect of ABA and iCB in tomato plants, we performed RNA-seq analysis of mock-, 10 uM ABA- or 10 uM iCB-treated plants. Differential gene expression analysis between mock- and ABA-treated or iCB-treated seedlings was done with DESeq2 and genes with an absolute value of log2 fold change (log2FC) > 1 or (log2FC) < -1 and p-adjusted value (padj) < 0.05 were selected. iCB upregulated and downregulated genes represent almost all the ABA-responsive genes, which reflects the activation of PYL1-like and PYL4-like and PYL8-like ABA receptors in tomato seedlings.
2025-08-25 | GSE279431 | GEO
Project description:In Arabidopsis, protein kinases from SnRK2 subclass I and III are considered to be mainly osmotic- and ABA- responsive, respectively. In this work we shed light on the role of SnRK2.4 kinase, a member of subclass I, in shaping the plant root architecture in response to exogenous ABA. We showed that SnRK2.4 is active in control conditions and upon ABA treatment, with a higher ABA sensitivity than SnRK2.2 and SnRK2.3 from class III concerning lateral root inhibition and root primordia emergence. To get insights into the molecular substrates of SnRK2.4, we compared the transcriptome, the proteome and phosphoproteome of wild-type plant to that of snrk2.4 mutants in control conditions and after 1 µM ABA treatment. Our phosphoproteomic analysis, that described 3858 unique phosphopeptides corresponding to 1820 phosphoproteins, revealed that 186 and 277 proteins were under phosphorylated in snrk2.4 mutants, in control conditions and upon ABA treatment, respectively. A regulation by SnRK2.4 of membrane transporters and cell-to-cell communication was highlighted in both conditions. By contrast, in response to ABA, SnRK2.4 specifically induced a decreased cellular abundance of RNA-helicases, thus, putatively interfering with mRNA splicing. It also modulated the phosphorylation of proteins putatively involved in the attenuation of ABA signaling, in lipid signaling and in cell wall biosynthesis, via an intricate PKs cascade mainly including members of CDPKs. This work pinpoints SnRK2.4 as an atypical ABA responsive SnRK2 involved in fundamental aspects of cell physiology.
2025-10-06 | PXD061019 | Pride
Project description:To compare the genome-wide transcriptional effect of ABA and iSB09 in tomato plants, we performed RNA-seq analysis of mock-, 10 uM ABA- or 20 uM iSB09-treated plants. Differential gene expression analysis between mock- and ABA-treated or iSB09-treated seedlings was done with DESeq2 and genes with an absolute value of log2 fold change (log2FC) > 1 or (log2FC) < -1 and p-adjusted value (padj) < 0.05 were selected. iSB09 upregulated and downregulated genes represent a subset of the ABA-responsive genes, which reflects the activation of PYL1-like and PYL4-like ABA receptors in tomato seedlings. Additionally, to compare the genome-wide transcriptional effect of ABA and iCB in tomato plants, we performed RNA-seq analysis of mock-, 10 uM ABA- or 10 uM iCB-treated plants. Differential gene expression analysis between mock- and ABA-treated or iCB-treated seedlings was done with DESeq2 and genes with an absolute value of log2 fold change (log2FC) > 1 or (log2FC) < -1 and p-adjusted value (padj) < 0.05 were selected. iCB mimics ABA transcriptional response through activation of the three subfamilies of ABA receptors.
2024-07-22 | GSE256238 | GEO
Project description:iCB elicits ABA-responsive gene expression in Arabidopsis thaliana seedlings
| PRJNA1172690 | ENA
Project description:This study was designed to identify changes in gene expression when corn was placed under various related stresses including being grown with a competing weed (canola) to the V4 or V8 stage, or when 40% shade cloth was present to the V4 or V8 stage, or under low nitrogen (no added nitrogen fertilizer), or under weed/shade free fertilized control conditions. In all 5 treatments and the control, samples were harvested at V8. Mechanisms underlying early season weed stress on crop growth are not well described. Corn vegetative growth and development, yield, and gene expression response to nitrogen (N), light (40% shade), and weed stresses were compared with the response of nonstressed plants. Vegetative parameters, including leaf area and biomass, were measured from V2 toV12 corn stages. Transcriptome (2008) or quantitative Polymerase Chain Reaction (q PCR) (2008/09) analyses examined differential gene expression in stressed versus nonstressed corn at V8. Vegetative parameters were impacted minimally by N stress although grain yield was 40% lower. Shade, present until V2, reduced biomass and leaf area > 50% at V2 and, at V12, recovering plants remained smaller than nonstressed plants. Grain yields of shade-stressed plants were similar to nonstressed controls, unless shade remained until V8. Growth and yield reductions due to weed stress in 2008 were observed when weeds remained until V6. In 2009, weed stress at V2 reduced vegetative growth, and weed stress until V4 or later reduced yield. Principle component analysis of differentially expressed genes indicated that shade and weed stress had more similar gene expression patterns to each other than to nonstressed or low N stressed tissues. Weed-stressed corn had 630 differentially expressed genes compared with the nonstressed control. Of these genes, 259 differed and 82 were shared with shade-stressed plants. Corn grown in N-stressed conditions shared 252 differentially expressed genes with weed-stressed plants. Ontologies associated with light/photosynthesis, energy conversion, and signaling were down-regulated in response to all three stresses. Although shade and weed stress clustered most tightly together, only three ontologies were shared by these stresses, O-methyltransferase activity (lignification processes), Poly U binding activity (post-transcriptional gene regulation), and stomatal movement. Based on both morphologic and genomic observations, results suggest that shade, N, and weed stresses to corn are regulated by both different and overlapping mechanisms.
2011-05-09 | GSE29132 | GEO
Project description:Shade avoidance syndrome (SAS) is a strategy of major adaptive significance that includes the elongation of vegetative structures and leaf hyponasty. Major transcriptional rearrangements underlie for the reallocation of resources to elongate vegetative structures and redefine the plant architecture under shade to compete for photosynthesis light. BBX28 is a transcription factor involved in seedling de-etiolation and flowering in Arabidopsis thaliana, but its function in the SAS is completely unknown. Here we studied the function of BBX28 in the regulation of gene expression under simulated shade conditions.
2024-03-15 | GSE217723 | GEO