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E-GEOD-35700

ABSTRACT: Expression data from low Red:Far-Red ratio and Jasmonic Acid crosstalk in Arabidopsis

OTHER RELATED OMICS DATASETS IN: PRJNA152037

PROVIDER: E-GEOD-35700 | ExpressionAtlas | 2015-11-27

REPOSITORIES: ExpressionAtlas

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			Action	DRS
	E-GEOD-35700-analysis-methods.tsv	Tabular
	E-GEOD-35700-atlasExperimentSummary.Rdata	Rdata
	E-GEOD-35700-configuration.xml	Xml
	E-GEOD-35700-percentile-ranks.tsv	Tabular
	E-GEOD-35700.condensed-sdrf.tsv	Tabular

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Expression data from low R:FR - JA crosstalk in Arabidopsis

2012-05-01 | GSE35700 | GEO

Activation of a singlet oxygen signaling pathway by competition cues in Arabidopsis thaliana

Project description:The goal of this work was to investigate oxidative stress responses of Arabidopsis to low red to far-red ratios of light as a signal of competition using a biological weedy and an artificial source of far-red light. More specifically, elucidation of the signaling role of singlet oxygen in Arabidopsis under low red-to far-red light environments was the major objective of this work. Oxidative stress responses of Arabidopsis to low red (R) to far-red (FR) signals (R:FR ≈ 0.3), generated by a biological weedy and an artificial source of FR light, were compared with a weed-free control (R:FR ≈1.4). In the low R:FR treatments, induction of the shade avoidance responses coincided with increased singlet oxygen (1O2) production and decreased level of superoxide and superoxide dismutase activity. Although the increase of 1O2 was not due to protochlorophyllide accumulation and did not result in cell death, treatments with the 1O2 generator 5-aminolevulinic acid increased sensitivity to cell death. Transcriptome responses minimally resembled those reported in four Arabidopsis 1O2 generating systems such that only few genes (6 out of 1931) were consistently up-regulated supporting the specificity of 1O2 signaling. Moreover, suppressors of jasmonate accumulation, including the 1O2-responsive amidohydrolase ILL6, the sulfotransferase ST2a, which are involved in prioritization of elongation growth versus defense were consistently up-regulated. Our data support a model in which photoreceptors connect low R:FR light cues to the JA signaling pathway. Repression of bioactive JAs via the amidohydrolase ILL6, and sulfotransferase ST2a may promote the shade avoidance (versus defense) and 1O2 acclimation (versus cell death) responses to competition cues.

2022-09-14 | GSE213185 | GEO

Genome-wide Binding Site Analysis of FAR-RED ELONGATED HYPOCOTYL 3 Reveals Its Novel Function in Arabidopsis Development

Project description:This SuperSeries is composed of the following subset Series: GSE30711: ChIP-Seq data from Arabidopsis thaliana under dark and far-red light GSE30712: Expression data from Arabidopsis thaliana under dark and far-red light Refer to individual Series

2011-12-31 | E-GEOD-30713 | biostudies-arrayexpress

Expression data from low R:FR - JA crosstalk in Arabidopsis

Project description:Low reduced red:far-red ratio [R:FR] signaling through phytochromes induces shade avoidance responses, including petiole elongation. Jasmonic acid-mediated defense against herbivores and pathogens is inhibited under these conditions. Using microarrays we studied the crosstalk between low R:FR and JA at the global gene expression level in Arabidopsis thaliana. Plants were exposed for 2 h. to the following treatments: high R/FR with mock spray, low R/FR with mock spray, high R/FR with JA spray, low R/FR with JA spray. Gene expression was determined in petioles.

2012-04-30 | E-GEOD-35700 | biostudies-arrayexpress

Arabidopsis thaliana

Project description:Expression data from Arabidopsis thaliana under dark and far-red light

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Arabidopsis thaliana

Project description:Expression data from Col-0 and pil5 imbibed seeds after far-red or far-red/red light irradiation.

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Arabidopsis thaliana

Project description:ChIP-Seq data from Arabidopsis thaliana under dark and far-red light

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Transcription profiling time course experiment performed over 24 hours to look at the effects on gene expression of exposure to low red:far-red ratio light in Arabidopsis thaliana plants

Project description:This experiment was a time course performed over 24 hours to look at the effects on gene expression of exposure to low red:far-red ratio light in Arabidopsis thaliana plants. In this way genes involved in the shade avoidance response might be identified. This experiment was designed for gene identification only and containes no replicates,genes identified were verified by quantitative PCR for publication.

2013-01-30 | E-MEXP-34 | biostudies-arrayexpress

ChIP-Seq data from Arabidopsis thaliana under dark and far-red light

Project description:FAR-RED ELONGATED HYPOCOTYL 3 (FHY3) and its homolog FAR-RED IMPAIRED RESPONSE 1 (FAR1) are two transposase-derived transcription factors initially identified as the key components in phytochrome A signaling and recently shown to function in the circadian clock. However, whether FHY3 and FAR1 are involved in other processes of plant development remains largely unknown. Here, we explored chromatin immunoprecipitation-based sequencing (ChIP-seq) analysis to identify 1745 and 1171 FHY3 direct binding target genes in darkness and far-red light conditions, respectively in the Arabidopsis thaliana genome. This analysis revealed that FHY3 preferentially binds to the gene promoters through the previously identified typical FHY3/FAR1 binding motif. Interestingly, FHY3 also binds to two novel motifs in the 178-bp repeats of the Arabidopsis centromere regions in vivo. Comparison between the ChIP-seq and microarray data indicates that FHY3 regulates the expression of 196 and 85 genes in dark and far-red respectively by directly binding to their promoters. FHY3 also co-regulates a number of common target genes with PHYTOCHROME INTERACTING FACTOR 3-LIKE 5 (PIL5) and ELONGATED HYPOCOTYL 5 (HY5). Moreover, our genome-wide identification of FHY3 direct target genes ultimately led to the discovery and validation of a new role of FHY3 in controlling chloroplast development, by directly activating the expression of ACCUMULATION AND REPLICATION OF CHLOROPLASTS5 (ARC5), a key gene regulating chloroplast constriction and division. Taken together, our data suggest that FHY3 is involved in regulating multiple facets of plant development, thus providing new insights into the functions of this type of transposase-derived transcription factors.

2011-08-02 | GSE30711 | GEO

Transcription profiling of Arabidopsis sav mutants

Project description:Plants grown at high densities perceive a decrease in the red to far-red (R:FR) ratio of incoming light, resulting from absorption of red light by canopy leaves and reflection of far-red light from neighboring plants. These changes in light quality trigger a series of responses known collectively as the shade avoidance syndrome. During shade avoidance, stems elongate at the expense of leaf and storage organ expansion, there is reduced branching, and flowering is accelerated. We identified several loci in Arabidopsis, mutations in which lead to plants defective in multiple shade avoidance outputs. Here we describe SAV3, an aminotransferase, and show that SAV3 catalyzes the formation of indole-3-pyruvic acid (IPA) from L-tryptophan (L-Trp), the first step in a previously proposed, but uncharacterized, auxin biosynthetic pathway. This pathway can be rapidly deployed to biosynthesize auxin at the high levels required to initiate the multiple changes in body plan associated with shade avoidance. Experiment Overall Design: Wild type Col-0, sav3-2 and sav1-1 seedlings were used here. They were treated with or without 1hr of low R:FR light (R:FR ratio=0.7). Three independent biological replicates were used.

2008-06-16 | E-GEOD-9816 | biostudies-arrayexpress

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