Genome-wide effect of BBX28 on the transcriptional response under shade in Arabidopsis thaliana
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ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE217723 | GEO | 2024/03/15
REPOSITORIES: GEO
Similar Datasets
Project description:Arabidopsis is a shade avioding plant. Under simulated shade light with reduced red-to-far red (R:FR) ratio around 0.7, hypocotyls of Arabidopsis seedlings elongate, which is one of the typical shade avoidance responses.We discovered that when the R:FR ratio further decreases to around 0.1 (strong shade), the shade-induced elongation of hypocotyl is abolished and phytochrome A (phyA) mediates this response.In this study, we aim to examine the difference between shade and strong shade treatment and uncover the role of phyA in regulating the shade avoidance responses.
2019-12-21 | GSE55899 | GEO
Project description:For shade-intolerant species, shade light indicates the close proximity of neighboring plants and triggers the shade avoidance syndrome (SAS), which causes exaggerated growth and reduced crop yield. We report that nonsecreted ROT FOUR LIKE (RTFL)/DEVIL (DVL) peptides negatively regulate the SAS by repressing the activities of BRASSINOSTEROID SIGNALING KINASEs (BSKs) and PHYTOCHROME INTERACTING FACTOR 4 (PIF4) in Arabidopsis. To identify RTFL function during SAS, we performed RNA-seq to search for differentially expressed genes (DEGs) by comparing transcript levels between Col-0 and dvl1-1D, bsk36, or pif47 seedlings during white light and shade conditions.
2023-09-28 | GSE226205 | GEO
Project description:For shade-intolerant plants, changes in light quality indicative of competition from neighboring plants trigger shade avoidance syndrome (SAS). PYHTOCHROME-INTERACTING FACTOR 7 is the major transcriptional regulator of SAS in Arabidopsis. However, the epigenetic reprogramming under shade is poorly understood. To identify the histone chaperone ASF1 and HIRA function during SAS, we performed transcriptome deep sequencing (RNA-seq) to search for differentially expressed genes (DEGs) by comparing transcript levels between Col-0 and pif7-1, asf1ab, or hira-1 seedlings during white light and shade conditions. Our data shown that histone chaperone ASF1, through interacting with PIF7 and helping of HIRA, positively regulates shade-induced genes expression.
2023-01-30 | GSE189669 | GEO
Project description:In seedlings, the induction of shade avoidance syndrome (SAS) involves a rapid up-regulation for known shade marker genes and subsequently activates an interacting network of various hormones that will eventually lead to cell elongation. We found that the B-box protein AtBBX24 have positive effects on the SAS (positive regulators). Global expression analysis of col and bbx24 seedlings reveals that a large number of genes involved in hormonal signaling pathways are positively regulated by BBX24 in response to simulated shade.
2015-01-08 | GSE64755 | GEO
Project description:In seedlings, the induction of shade avoidance syndrome (SAS) involves a rapid up-regulation for known shade marker genes and subsequently activates an interacting network of various hormones that will eventually lead to cell elongation. We found that the B-box protein AtBBX24 have positive effects on the SAS (positive regulators). Global expression analysis of col and bbx24 seedlings reveals that a large number of genes involved in hormonal signaling pathways are positively regulated by BBX24 in response to simulated shade. The microarray experiment consisted in a factorial design comprising two genotypes (col and bbx24-1) and two light treatments (white light and simulated shade). RNA material was extracted from 7-day-old seedlings. Two replicates per treatment were performed using Affymetrix Arabidopsis ATH1 GeneChips. RNA was prepared, labeled and hybridized in accordance with the manufacturerM-bM-^@M-^Ys instructions. Data were normalized and genes with M-bM-^@M-^XabsentM-bM-^@M-^Y calls and a signal of <50 units in all replicate experiments were filtered out. Significantly differentially expressed genes were identified by performing profile analysis using Significance Analysis of Microarrays (SAM; Tusher et al., 2001).
2015-01-08 | E-GEOD-64755 | biostudies-arrayexpress
Project description:Many of shade-intolerant or sun-loving plants grown in close proximity experience a change in light quality and quantity, which leads to transcriptional reprogramming and consequently shade avoidance syndrome (SAS). Despite the importance of phosphorylation-dependent signaling for cellular physiology, the phosphorylation events during SAS are largely unknown. Here, we carried out a survey of shade-regulated protein phosphorylation events by a large-scale mass spectrometry-based quantitative phosphoproteomics approach. The activity of protein phosphatase 2A (PP2A) was specifically activated by shade treatment. Thereinto, shade de-phosphorlated a group of basic leucine zipper (bZIP) transcription factor by PP2A-b’ηθγζ. This study elucidates a previously unidentified mechanism by which the PP2A-bZIPs regulatory module integrates shade signal, and thus uncovers a phosphorylation strategy for the rapid response to changes of environment.
2024-04-25 | PXD041796 | JPOST Repository
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. Keywords: shade avoidance auxin brassinosteroid
2008-04-01 | GSE9816 | GEO
Project description:Unlike the situation in animals, the final morphology of the plant body is highly modulated by the environment. During Arabidopsis development, intrinsic factors provide the framework for basic patterning processes. CLASS III HOMEODOMAIN LEUCINE ZIPPER (HD‐ZIPIII) transcription factors are involved in embryo, shoot and root patterning and during vegetative growth regulate several polarity set‐up processes such as in leaves and the vascular system. Here we show that besides being involved in basic patterning, HD‐ZIPIII transcription factors also have a critical role in controlling elongation growth that is induced when plants experience shade. By using a ChIP‐Seq approach, we have identified several direct target genes of the HD‐ZIPIII transcription factor REVOLUTA (REV). We show that REV acts upstream of auxin biosynthesis and directly regulates several HAT transcription factors that control shade avoidance responses in Arabidopsis. Plants in which HD‐ZIPIII genes are mutated show altered responses to shade revealing that the basic patterning machinery also regulates adaptive development. Thus, HD-ZIPIII transcription factors contribute to shade signaling and act upstream of both auxin and HAT activation.
2012-06-01 | GSE26722 | GEO
Project description:Unlike the situation in animals, the final morphology of the plant body is highly modulated by the environment. During Arabidopsis development, intrinsic factors provide the framework for basic patterning processes. CLASS III HOMEODOMAIN LEUCINE ZIPPER (HD‐ZIPIII) transcription factors are involved in embryo, shoot and root patterning and during vegetative growth regulate several polarity set‐up processes such as in leaves and the vascular system. Here we show that besides being involved in basic patterning, HD‐ZIPIII transcription factors also have a critical role in controlling elongation growth that is induced when plants experience shade. By using a ChIP‐Seq approach, we have identified several direct target genes of the HD‐ZIPIII transcription factor REVOLUTA (REV). We show that REV acts upstream of auxin biosynthesis and directly regulates several HAT transcription factors that control shade avoidance responses in Arabidopsis. Plants in which HD‐ZIPIII genes are mutated show altered responses to shade revealing that the basic patterning machinery also regulates adaptive development. Thus, HD-ZIPIII transcription factors contribute to shade signaling and act upstream of both auxin and HAT activation. A. thaliana REVOLUTA ChIP-seq w control
2012-06-01 | E-GEOD-26722 | biostudies-arrayexpress
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