Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A role for PICKLE in the regulation of cold stress response in Arabidopsis

ABSTRACT: Our study showed that the CHD3 protein PKL plays a role in the regulation of cold stress response likely via the regulation of chlorophyll accumulation under low temperature conditions. Our results suggest that PKL may regulate cold response partly via a CBF3-mediated pathway. Besides, our results reveal that the PKL gene is also involved in the regulation of drought and salt stress resistance.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE127819 | GEO | 2019/03/06

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Project description:The evolution and diversification of proteins capable of remodelling domains has been critical for transcriptional reprogramming during cell fate determination in multicellular eukaryotes. Chromatin remodelling proteins of the CHD3 family have been shown to have important and antagonistic impacts on seed development in the model plant, Arabidopsis thaliana, yet the basis of this functional divergence remains unknown. In this study, we demonstrate that genes encoding the CHD3 proteins PICKLE (PKL) and PICKLE-RELATED 2 (PKR2) originated from a duplication event during the diversification of crown Brassicaceae, and that these homologues have undergone distinct evolutionary trajectories since this duplication, with PKR2 fast-evolving under positive selection, while PKL is evolving under purifying selection. We find that the rapid evolution of PKR2 under positive selection reduces the encoded protein’s intrinsic disorder, possibly suggesting a tertiary structure configuration which differs from that of PKL. Our whole genome transcriptome analysis of gene expression in seeds of pkr2 and pkl mutants reveals that they act antagonistically on the expression of specific sets of genes, providing a basis for their differing roles in seed development. Our results provide insights on gene duplication and neofunctionalization can lead to differing and antagonistic selective pressures on transcriptomes during plant reproduction, as well as on the evolutionary diversification of the CHD3 family within seed plants.

2023-09-06 | GSE236025 | GEO

Transcription profiling of Arabidopsis pickle mutants

Project description:Wild type, pkl, pkr2 and pkl pkr2 plants were grown, and gene expression in roots was compared at the age of 5 days.

2009-08-19 | E-MEXP-2140 | biostudies-arrayexpress

Identify differentially expressed genes in 14-day-old pkl seedlings

Project description:CHD3 proteins are ATP-dependent chromatin remodeling factors that are components of diverse multisubunit complexes that can either repress or activate gene expression. In plants, the CHD3 protein PICKLE (PKL) is necessary for repression of seed-specific genes during germination and promotes deposition of the repressive epigenetic mark trimethylation of histone H3 lysine 27 (H3K27me3). It is unknown, however, if PKL acts directly at H3K27me3-enriched loci. We undertook a microarray analysis of 14-day-old plants and found that PKL continues to play an important role in expression of H3K27me3-enriched genes and in specification of developmental identity after germination. We used microarray to identify genes that are differentialy expressed in 14-day-old pkl seedlings and used chormatin immunoprecipitation to identify genes that are the direct targets of PKL. Wild-type (Col-0) and pkl-1 seedlings were grown on 1/2 MS plates with constant light and harvsted after 14-day growth. Three biological replicates.

2012-01-01 | E-GEOD-31639 | biostudies-arrayexpress

Effect of uniconazole-P on wt and pkl mutant germinating seeds

Project description:Relative expression data from germinating seeds of Columbia (wt), the pkl mutant (pkl), Columbia plus uniconazole-P (Uwt) and the pkl-mutant plus uniconazole-P (Upkl). Each experimental condition (wt, pkl, Uwt and Upkl) has four true replicates for a total of 16 chips. Keywords = CHD3 Keywords = chromatin remodeling factors Keywords = developmental transition Keywords = embryo Keywords = seed germination Keywords: other

2003-07-07 | GSE277 | GEO

Identify differentially expressed genes in 14-day-old pkl seedlings

2012-01-01 | GSE31639 | GEO

RNA-seq data for Arabidopsis cbfs-1

Project description:In Arabidopsis, CBFs transcription factors (CBF1, CBF2 and CBF3) play fundamental roles in plant cold tolerance, especially in cold-acclimation. By employing CRISPR/Cas9, we knocked out CBF1 and CBF2 simultaneously in cbf3 background and generated cbfs triple mutant. This mutant facilitated the discovery of CBF-regulated genes. In this study, Arabidopsis 14-d-old Col-0 and cbfs mutant were treated with cold stress (4 degree centigrade) for 0, 3 and 24 hours. The seedlings were harvested for total RNA extraction and sequencing.

2019-05-07 | GSE130729 | GEO

VAL1/2 recruit PKL to target sites in arabidopsis genome

Project description:PICKLE (PKL), a Chromodomain Helicase DNA binding domain type 3-type (CHD3) chromatin remodeler, noted for an embryonic structure called pickle root in primary root tip in pkl mutant, has been studied for decades. we obtained a comprehensive genome occupancy of PKL by Chromatin immunoprecipitation-sequencing (ChIP-seq), and found PKL co-occupy with the major repressors of seed maturation program, VIVIPAROUS1/ABI3-LIKE1/2 (VAL1/2) in genome. Furthermore, PKL physically interacts with VAL1/2 in vivo and phenotype and transcriptome data indicated that PKL and VAL1/2 function in a common pathway. Moreover, ChIP-seq and ChIP-qPCR results showed that VAL1/2 are necessary for the recruitment of PKL to co-target genes

2023-05-10 | GSE186157 | GEO

Transcriptome and metabolome changes in Chinese cedar during cold acclimation reveal the roles of flavonoids in needle discoloration and cold resistance

Project description:Cryptomeria fortunei growth and development are usually affected by low temperatures. Despite the evergreen nature of this species, most needles turn yellowish-brown in cold winters. The underlying discoloration mechanisms that cause this phenomenon in response to cold acclimation remain poorly understood. Here, we measured the pigment content and ultrastructure of normal wild-type (Wt) and evergreen mutant (GM) C. fortunei needles and performed integrated transcriptomic and metabolomic analyses to explore potential discoloration mechanisms. The results showed that the needle chlorophyll content of these two genotypes decreased in winter. Wt needles showed greater decrease in the chlorophyll content and local destruction of chloroplast ultrastructure, and contained larger amounts of flavonoids than GM needles, as shown by metabolomics analysis. We subsequently identified key differentially expressed genes in the flavonoid biosynthesis pathway and observed significantly upregulated flavonol synthase (FLS) expression in Wt needles compared to GM needles, that significantly increased the anthoxanthin (flavones and flavonols) content, which is likely a key factor underlying the difference in needle color between these two genotypes. Therefore, flavonoid metabolism may play important roles in the cold resistance and needle discoloration of C. fortunei, and our results provide an excellent foundation for the molecular mechanism of C. fortunei in response to cold stress.

2022-08-12 | MTBLS3184 | MetaboLights

A role for PICKLE in the regulation of cold stress response in Arabidopsis

Project description:A role for PICKLE in the regulation of cold stress response in Arabidopsis

| PRJNA525452 | ENA

The impact of cold priming on the light and cold regulation of gene expression in Arabidopsis thaliana

Project description:We analysed the effect of cold priming on cold and high light regulation of gene expression. 5 days after the first cold treatment the primary stress response was widely reset. Then, a second (triggering) cold stimulus (24 h 4 °C) and a triggering high-light stimulus (2 h 800 µmol quanta m-2 s-1), which regulate many stress responsive genes in the same direction in naïve plants, caused widely specific and even inverse regulation of priming-responsive genes.

2020-06-08 | GSE151749 | 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