Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

PIF7 is the master regulator of thermomorphogenesis in shade [ChIP-seq]

ABSTRACT: The size and shape of plant organs are highly responsive to environmental conditions. The plant's embryonic stem, or hypocotyl, displays phenotypic plasticity, in response to light and temperature. The, hypocotyl of shade avoiding species elongate to outcompete neighbouring plants and secure access to sunlight. Similar elongation occurs in high temperature. PHYTOCHROME-INTERACTING FACTORS (PIFs) family transcription are known to be importenet players in these responses. However, it is poorly understood how environmental light and temperature interact to affect plants development. We found that low R/FR combined with warm temperature produces a synergistic hypocotyl growth response that dependent on PIF7 and the hormone auxin. We demonstrate that additional, unknown factor/s must be working downstream of the phyB-PIF-auxin module. As shade responses are known to affect yield, susceptibility to pathogens, and fruit quality in many species, our findings will improve the predictions of how plants will respond to increased ambient temperatures when grown at high density, a condition in which mutual shading occurs.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE205208 | GEO | 2022/07/26

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

PIF7 is the master regulator of thermomorphogenesis in shade [RNA-seq]

Project description:The size and shape of plant organs are highly responsive to the local environmental conditions. The embryonic stem, or hypocotyl, of the plant is one such organ that displays impressive phenotypic plasticity, and its length is affected by both light and temperature. After sensing surrounding vegetation, hypocotyls of shade avoiding species elongate to outcompete neighbouring plants and secure access to sunlight. A similar elongation response occurs when the plants are grown in high ambient temperatures. Previous studies have shown that this response is mediated by a family of transcription factors called PHYTOCHROME-INTERACTING FACTORS (PIFs). However, it is poorly understood how environmental light and temperature interact to affect plants at the morphological and molecular levels. Here, we examine the genetic and molecular basis of the response to low R/FR under warm ambient temperatures. We found that low R/FR combined with warm temperature dominantly regulate by PIF7 and exhibit a synergistic effect on hypocotyl growth, greater than either stimulus alone. While the synergistic response was dependent on PIF7 and the plant hormone auxin, we demonstrate that additional, yet unknown key factor/s must be involved, likely working downstream of the phyB-PIF-auxin module. As shade responses are known to affect crop yield and fruit quality in many species, our findings will improve the predictions of how plants will respond to increased ambient temperatures when grown at high density, a condition in which mutual shading occurs. In addition, we point out key factors in this response that can potentially be modulated to minimize the negative effect on yield.

2022-07-26 | GSE196725 | 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

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

Auxin signaling in the epidermis regulates stem growth via interactions with the brassinosteroid pathway

Project description:Growth of a complex multicellular organism requires coordinated changes in diverse cell types. These cellular changes generate organs of the correct size, shape and functionality. During plant development, the growth hormone auxin induces stem elongation; however, which cell types of the stem perceive the auxin signal and contribute to organ growth is poorly understood. Here, we show that auxin signalling is required in many cell types for correct hypocotyl stem growth, with a key role for the epidermis. Combining genetic manipulations in Arabidopsis thaliana with transcriptional profiling of the hypocotyl epidermis from Brassica rapa, we show that auxin functions in the epidermis in part by inducing activity of the locally-acting, growth-promoting brassinosteroid pathway. Our findings clarify cell-specific auxin function in the hypocotyl, and highlight the complexity of cell-type interactions within a growing organ. We performed whole-genome transcriptome (mRNA-Seq) on 5 d-old W light-grown Arabidopsis thaliana plants (CER6pro>>axr3-1::mCit experimental plants and UAS::axr3-1::mCit hemizygous control plants; whole-seedling tissue) treated for 4 h W light or low R:FR shade. In addition, we performed mRNA-Seq on 4 d-old Brassica rapa plants (FPsc strain) treated for 9 h W light or shade. Brassica tissues collected were hypocotyl epidermal peels or whole hypocotyls.

2016-06-30 | E-GEOD-79881 | biostudies-arrayexpress

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

Temporal and spatial frameworks supporting plant responses to vegetation proximity

Project description:After perception of vegetation proximity by the phytochrome photoreceptors, shade-avoider plants initiate a set of responses known as the Shade Avoidance Syndrome (SAS). Shade perception by the phytochrome B (phyB) photoreceptor unleashes the PHYTOCHROME INTERACTING FACTORs (PIFs) and initiates SAS responses. In Arabidopsis thaliana seedlings, shade perception involves rapid and massive changes in gene expression, increases auxin production and promotes hypocotyl elongation. Other components, such as phyA and ELONGATED HYPOCOTYL 5 (HY5), also participate in the shade regulation of the hypocotyl elongation response by repressing it. However, it remains unclear why and how so many regulators with either positive or negative activities modulate the same response. Our physiological, genetic, cellular and transcriptomic analyses showed that (1) these components are organized in two main branches or modules (phyA/HY5 and PIFs/HFR1/SAV3) and (2) the connection between them is dynamic and changes with the time of shade exposure. We propose a model for the regulation of shade-induced hypocotyl elongation in which the temporal and spatial functional importance of the various SAS regulators analyzed in here helps to explain the co-existence of differentiated regulatory branches with overlapping activities. Despite the temporal differences observed between phyA, HY5 and PIFs/HFR1/SAV3, their activities overlap and eventually converge in controlling hypocotyl elongation. Hence, we aimed to further investigate possible convergence points between these two groups of regulators.To expand our understanding of the role and interaction of HY5 and PIF4, PIF5 and PIF7 (PIF457) activities, we carried out RNA sequencing (RNA-seq) of seedlings exposed to different times of shade exposure of four genotypes: wild-type (Col-0), the single mutant hy5, the triple pif457 and the quadruple hy5 pif457.

2024-08-26 | GSE268032 | GEO

PIF7 DNA binding in response to long days with daily oscillating temperatures in Arabidopsis thaliana

Project description:This study aimed to characterise the genome-wide PIF7-mediated responses of Arabidopsis thaliana seedlings to long photoperiods with a warm 27°C midday in comparison to long photoperiods at constant 17°C. Transcriptomic responses were observed in Col-0 wild-type and pif7-1 loss-of-function mutants investigate the potential contribution of the transcription factor PIF7 to the warm temperature response under the described conditions. In parallel, ChIP-seq of a PIF7-MYC-expressing line under the same conditions was employed to investigate global DNA binding changes of PIF7 in response to a change in temperature.

2020-02-29 | GSE127745 | GEO

MicroRNA156 conditions auxin sensitivity to enable growth plasticity in response to environmental changes in Arabidopsis (RNA-Seq)

Project description:MicroRNAs (miRNAs) play diverse roles in plant development, but whether and how miRNAs participate in thermomorphogenesis remains ambiguous. Here we show that HYPONASTIC LEAVES1 (HYL1) – a key component of microRNA biogenesis – acts downstream of the thermal regulator PHYTOCHROME INTERACTING FACTOR 4 in temperature-dependent plasticity of hypocotyl growth in Arabidopsis. A hyl1-2 suppressor screen identified a dominant dicer-like1 (dcl1) allele, dcl1-24, that rescues hyl1-2’s defects in miRNA biosynthesis and warm temperature-induced hypocotyl elongation. Genome-wide miRNA and transcriptome analysis reveal microRNA156 (miR156) and its target SQUAMOSA PROMOTER-BINDING-LIKE 9 (SPL9) as critical regulators of thermomorphogenesis. Surprisingly, perturbation of the miR156/SPL9 module disengages seedling responsiveness to warm temperatures by impeding auxin sensitivity. Moreover, the miR156-dependent auxin sensitivity also operates in the shade avoidance response at lower temperatures. Thus, these results unveil the miRNA156/SPL9 module as a previously-uncharacterized genetic circuitry that enables plant growth plasticity in response to environmental temperature and light changes.

2023-02-11 | GSE216360 | GEO

MicroRNA156 conditions auxin sensitivity to enable growth plasticity in response to environmental changes in Arabidopsis (miRNA-Seq)

Project description:MicroRNAs (miRNAs) play diverse roles in plant development, but whether and how miRNAs participate in thermomorphogenesis remains ambiguous. Here we show that HYPONASTIC LEAVES1 (HYL1) – a key component of microRNA biogenesis – acts downstream of the thermal regulator PHYTOCHROME INTERACTING FACTOR 4 in temperature-dependent plasticity of hypocotyl growth in Arabidopsis. A hyl1-2 suppressor screen identified a dominant dicer-like1 (dcl1) allele, dcl1-24, which rescues hyl1-2’s defects in miRNA biosynthesis and warm temperature-induced hypocotyl elongation. Genome-wide miRNA and transcriptome analysis reveal microRNA156 (miR156) and its target SQUAMOSA PROMOTER-BINDING-LIKE 9 (SPL9) as critical regulators of thermomorphogenesis. Surprisingly, perturbation of the miR156/SPL9 module disengages seedling responsiveness to warm temperatures by impeding auxin sensitivity. Moreover, the miR156-dependent auxin sensitivity also operates in the shade avoidance response at lower temperatures. Thus, these results unveil the miRNA156/SPL9 module as a previously-uncharacterized genetic circuitry that enables plant growth plasticity in response to environmental temperature and light changes.

2023-02-11 | GSE216361 | GEO

Gene expression profiling of 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. Keywords: shade avoidance auxin brassinosteroid

2008-04-01 | GSE9816 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data