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Epigenetic reprogramming orchestrates transcriptional responses in shade avoidance memory of Arabidopsis

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

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE226745 | GEO | 2024/07/29

REPOSITORIES: GEO

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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 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.

2023-01-30 | GSE189669 | GEO

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

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

2024-08-18 | GSE227154 | GEO

PHYTOCHROME-INTERACTING FACTOR 7-mediated epigenetic reprogramming promotes the transcriptional response to shade in Arabidopsis

Project description:ChIP-Seq were performed using 35S::GFP-ASF1A, pHTR13::HTR13-HA, pHTR5::HTR5-HA, and pHTR5::HTR5-HA/pif7-1 transgenic plants after white light and 1 hr shade treatment. Two biological replicates were prepared for each genotype of plants grown under light and shade conditions. High-confidence binding peaks with cut off fold change > 1.5 and P-value <0.01. Our data reveal that ASF1 directly regulating a subset of target genes of PIF7. Furthermore, shade-elicited gene activation is accompanied by H3.3 enrichment, which is mediated by the PIF7-ASF1 regulatory module.

2023-01-30 | GSE193955 | GEO

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

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

2015-01-08 | GSE64755 | GEO

ELONGATED HYPOCOTYL (HY5) AND HY5 HOMOLOG (HYH) maintain shade avoidance suppression in sunlight

Project description:We show that longer-term inhibition of shade avoidance in Arabidopsis is sustained by ELONGATED HYPOCOTYL 5 (HY5) and HY5 HOMOLOG (HYH) which, together, regulate transcriptional reprogramming of genes involved in hormone signalling and cell wall modification.

2023-06-07 | GSE192469 | GEO

A shade-induced long non-coding RNA promotes shade response through repressing the transcriptional induction of PHYTOCHROME A

Project description:A high-depth strand-specific RNA sequencing (ssRNA-seq) using 5-day-old white-light grown Col-0 and pif7-1 seedlings with additional 1 hr shade or white light treatment.

2023-03-16 | GSE210807 | GEO

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

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