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

ABSTRACT: 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.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE127745 | GEO | 2020/02/29

REPOSITORIES: GEO

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Genome-wide analysis of transcription and 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.

2020-06-02 | GSE124003 | GEO

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

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

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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

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

Project description: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.

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Genome-wide analysis of transcription and PIF7 DNA binding in response to long days with daily oscillating temperatures in Arabidopsis thaliana

Project description:Genome-wide analysis of transcription and PIF7 DNA binding in response to long days with daily oscillating temperatures in Arabidopsis thaliana

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Gene expression during hormone-induced shoot regeneration in Arabidopsis thaliana explants exposed to different temperatures

Project description:Many plants are able to regenerate upon cutting, and this process can be enhanced in vitro by incubating explants on hormone-supplemented media. While such protocols have been used for decades, little is known about the molecular details of how incubation conditions influence their efficiency. In this study, we show that warm temperature promotes both callus formation and shoot regeneration efficiency in Arabidopsis thaliana. Our RNA sequencing analysis unveil that this accompanied by the enhanced expression of several regeneration-associated genes, such as CUP-SHAPED COTYLEDON 1 (CUC1), encoding a transcription factor involved in shoot meristem formation, and ISOPENTENYLTRANSFERASE (IPT1) and YUCCA1/4 (YUC1/4), encoding key enzymes for cytokinin and auxin biosynthesis, respectively. Consistently, mutations in CUC1 and IPT1 or chemical inhibition of YUCs reduce the enhancement of shoot regeneration at warm temperature. When combined with ChIP sequencing analyses, our RNA sequencing data further reveal that histone variant H2A.Z is enriched on these differentially expressed loci at 17°C and that its occupancy level decreases when the ambient temperature increases to 27°C. This study thus unveil a new epigenetic mechanism that influences hormone-induced regeneration and brings further insights on how incubation temperature is a crucial parameter in optimizing protocols for in vitro tissue culture.

2022-02-15 | GSE176161 | GEO

Transcriptomic profiling by array of long-term thermal acclimation (2 months) at various temperatures in liver tissue of Pachycara brachycephalum

Project description:The Antarctic eelpout, Pachycara brachycephalum, is a member of the cosmopolitan fish family Zoarcidae, which comprises 284 species distributed all over the globe. Since the Antarctic realm is a highly constant habitat, the species P. brachycephalum was employed in a global approach to characterize thermal response mechanisms in terms of long-term cold- and warm acclimation. Specimen of P. brachycephalum were incubated for 2 months at six different temperatures: -1C, 0C (control), 3C, 5C, 7C, 9C. In each group 5 fish were selected for hybridization (except control: n=7). By comparing the features of control and treatment groups we addressed temperature dependent expression profiles in liver tissue.

2014-03-20 | E-MTAB-2252 | biostudies-arrayexpress

Facing warm temperatures during migration – cardiac mRNA responses of two adult sockeye salmon Oncorhynchus nerka populations to warming and swimming challenges

Project description:The main findings of the current study were that exposing adult sockeye salmon Oncorhynchus nerka to a warm temperature that they regularly encounter during their river migration induced an mRNA-level heat shock response that is exacerbated with swimming. Similar immune defense-related responses were also observed. Microarray analyses revealed that 347 genes were differentially expressed between the cold (12-13° C) and warm (18-19° C) treated fish (P < 0.01), with stress response (GO:0006950; P = 0.014) and response to fungus (GO:0009620; P = 0.003) elevated with warm treatment, while expression for genes involved in oxidative phosphorylation (GO:0006119; P = 0.0019) and electron transport chain (GO:0022900; P = 0.00043) increased in cold-treated fish. By studying single genes with RT-qPCR, warm treatment fish from the Chilko population of O. nerka induced expression of heat shock protein (hsp) 90α, hsp90β and hsp30, as well as interferon-inducible protein (P < 0.05). A Nechako population of O. nerka with a narrower thermal tolerance window than the Chilko population showed even more pronounced responses to the warm treatment. In conclusion, it appears that during their once-in-the-lifetime migration these adult sockeye salmon encounter conditions that induce several cellular defense mechanisms. As river temperatures continue to increase, it remains to be seen whether or not these cellular defenses provide enough protection for all sockeye salmon populations.

2013-12-15 | GSE50054 | GEO

Seasonal changes of gene expression of whole brain in Medaka fish (Oryzias latipes) LW

Project description:To examine the seasonal transcriptional landscape of medaka brain, we compared the gene expression of whole brain under SC (short-day and cool temperature conditions: 10 h light/14 h dark and 10 °C) and LW (long-day and warm temperature conditions: 14 h light/10 h dark and 26 °C) conditions.

2020-04-23 | GSE124985 | GEO

Seasonal changes of gene expression of whole brain in Medaka fish (Oryzias latipes) SC

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