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

ABSTRACT: 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.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE210807 | GEO | 2023/03/16

REPOSITORIES: GEO

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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

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

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

Two bHLH Transcription Factors, bHLH48 and bHLH60, Associate with PHYTOCHROME INTERACTING FACTOR 7 to Regulate Hypocotyl Elongation in Arabidopsis thaliana

Project description:A ChIP-Seq was performed using 35S::PIF7-Flash and 35S::bHLH60-Flag transgenic plants after 1 hr shade treatment. Approximately 6374 peaks (5262 genes) were considered as high-confidence of PIF7 binding peaks (Fold change > 2, q-value < 0.05). And 2278 peaks (2143 genes) were considered as high-confidence of bHLH60 binding peaks. The bound genes of PIF7 significantly overlapped with bHLH60-bound genes. And, the transcriptional levels of PIF7 and bHLH60 co-bound genes were also regulated by PIF7 and bHLH48/60. Our results indicated PIF7 and bHLH60 form a heterodimer to bind to promoters of the common target genes and regulate their expressions.

2021-12-08 | GSE156584 | GEO

Genome-wide transcriptome of the coleoptile and the first leaf treated by white light or shade in rice seedlings

Project description:Purpose: In order to figure out the tissue-specific mechanism in rice, we collected coleoptiles and the first leaves separately from the seedlings treated by 1 hr shade or white light for RNA sequencing.

2016-12-19 | GSE76051 | GEO

KANADI1-regulated genes in shade

Project description:RNA-Seq of Arabidopsis thaliana Col-0 and 35S::FLAG-GR-KAN1 plants grown in ambient light or shade.

2015-08-11 | GSE68684 | GEO

KANADI1-regulated genes in shade

Project description:RNA-Seq of Arabidopsis thaliana Col-0 and 35S::FLAG-GR-KAN1 plants grown in ambient light or shade. 8 samples (Col-0 wildtype, 35S::FLAG-GR-KAN1 each in shade or ambient light, each with mock or Dexamethasone treatment) with two technical replicates were sequenced.

2015-08-11 | E-GEOD-68684 | biostudies-arrayexpress

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

Central clock components modulate plant shade avoidance by directly repressing transcriptional activation activity of PHYTOCHROME-INTERACTING FACTORS

Project description:Light-environment signals, sensed by plant phytochrome (phy) photoreceptors, are transduced to target genes through direct regulation of PHYTOCHROME-INTERACTING FACTOR (PIF) transcription factor abundance and activity. Previous genome-wide DNA-binding and expression analysis has identified a set of genes that are direct targets of PIF transcriptional regulation. However, quantitative analysis of promoter occupancy versus expression level has suggested that unknown “trans factors” modulate the intrinsic transcriptional activation activity of DNA-bound PIF proteins. Here, using computational analysis of published data, we have identified PSEUDO-RESPONSE REGULATORS (PRR5 and PRR7) as displaying a high frequency of co-localization with the PIF proteins at their binding sites in the promoters of PIF Direct Target Genes (DTGs). We show that the PRRs function to suppress PIF-stimulated growth in the light and vegetative shade, and that they repress the rapid PIF-induced expression of PIF-DTGs triggered by exposure to shade. The repressive action of the PRRs on both growth and DTG expression requires the PIFs, indicating direct action on PIF activity, rather than a parallel antagonistic pathway. Protein interaction assays indicate that the PRRs exert their repressive activity by binding directly to the PIF proteins in the nucleus. These findings support the conclusion that the PRRs function as direct outputs from the core circadian oscillator, to regulate the expression of PIF-DTGs, through modulation of PIF transcriptional activation activity, thus expanding the roles of the multifunctional PIF signaling hub.

2020-09-01 | GSE136843 | GEO

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