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Effect of bZIP59 on transcriptional regulation during shade avoidance responses in Arabidopsis

ABSTRACT: Shade can trigger the shade avoidance syndrome (SAS) in shade-intolerant species,which cause exaggerated growth and affect crop yield.We report that Arabidopsis transcription factors bZIP59 negatively regulate SAS. To investigate the function of bZIP59 during SAS, we performed RNA-Seq of wild type Col-0 and a T-DNA insertion line bzip59 (SALK_024459) in while light and shade.

ORGANISM(S): Arabidopsis

PROVIDER: GSE227154 | GEO | 2024/08/18

REPOSITORIES: GEO

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De-phosphorylation of bZIP59 by PP2A ensures appropriate shade avoidance response in Arabidopsis

Project description:Shade can trigger the shade avoidance syndrome (SAS) in shade-intolerant species, which cause exaggerated growth and affect crop yield. We report that Arabidopsis transcription factors bZIP59 negatively regulate SAS. To identify direct targets of bZIP59 at the genome-wide level, we performed ChIP-Seq using ProbZIP59::bZIP59-GFP/bzip59 transgenic plants under white light or transferred to shade conditions for 2 hours. Our results indicated shade light dramatically increased the DNA binding ability of bZIP59, and shade-enhanced binding of bZIP59 majorly located around transcriptional start site (TSS) of genes.

2024-08-18 | GSE236101 | GEO

Shade-induced RTFL/DVL peptides negatively regulate the shade response by directly interacting with BSKs in Arabidopsis

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

Epigenetic reprogramming orchestrates transcriptional responses in shade avoidance syndrome of Arabidopsis

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.

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Global transcriptome analysis identifies shade avoidance-related genes regulated by BBX24 in Arabidopsis thaliana

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Global transcriptome analysis identifies shade avoidance-related genes regulated by BBX24 in Arabidopsis thaliana

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

PP2A mediates phosphorylation events during shade avoidance response in Arabidopsis

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

phytochrome A-mediated shade avoidance responses

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

PHYTOCHROME-INTERACTING FACTOR 7 and RELATIVE OF EARLY FLOWERING 6 act in shade avoidance memory in Arabidopsis

Project description:Shade avoidance helps plants maximize their access to light for growth under crowding. It is unknown, however, whether a priming shade avoidance mechanism exists that allows plants to respond more effectively to successive shade conditions. Here, we show that the shade-intolerant plant Arabidopsis can remember a first experienced shade event and respond more efficiently to the next event on hypocotyl elongation. The transcriptional regulator PHYTOCHROME-INTERACTING FACTOR 7 (PIF7) and the histone H3K27-demethylase RELATIVE OF EARLY FLOWERING 6 (REF6) were identified as being required for this shade avoidance memory. RNA-sequencing analysis revealed that shade induction of shade memory-related genes was impaired in the pif7 and ref6 mutants. Based on the enrichments of H3K27me3, REF6 and PIF7, we found that priming shade treatment induced PIF7 accumulation, which further recruited REF6 to demethylate H3K27me3 on the chromatin of certain memory-related genes, leading to a state poised for their transcription. Upon the second shade treatment, enhanced shade-mediated induction of these genes resulted in stronger hypocotyl growth responses. We conclude that the transcriptional memory mediated by epigenetic modification plays a key role in the ability of primed plants to remember previously experienced shade and acquire enhanced responses to recurring shade conditions.

2024-07-29 | GSE268785 | GEO

Epigenetic reprogramming orchestrates transcriptional responses in shade avoidance memory of Arabidopsis

Project description:An RNA-seq was conducted to investigate how REF6 and PIF7 participate in shade avoidance memory.

2024-07-29 | GSE226745 | GEO

Genome-wide effect of BBX28 on the transcriptional response under shade in Arabidopsis thaliana

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

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