A role for PICKLE in the regulation of cold stress response in Arabidopsis
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ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE127819 | GEO | 2019/03/06
REPOSITORIES: GEO
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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
Project description:In the field, abiotic stresses are rarely applied individually. Crops are often subjected to a combination of stresses. To date, no study has been performed on the proteomic investigation of the response of common wheat to a combination of drought and cold stresses. In this study, wheat seedlings exposed to drought-cold stress for 24 h showed inhibited growth, increased lipid peroxidation, relative electrolyte leakage, and soluble sugar contents. To determine the wheat protein response to drought-cold stress, iTRAQ-based quantitative proteomic and liquid chromatography tandem mass spectrometry (LC-MS/MS) methods were employed to determine the proteomic profiles of the roots and leaves of wheat seedlings exposed to drought-cold stress conditions. We identified 250 and 258 proteins with significantly altered abundance in the roots and leaves, respectively. These proteins were classified into several main groups, as follows: protein metabolism, stress/defense, carbohydrate metabolism, lipid metabolism, transcription-related processes, energy production, cell-wall and cytoskeleton metabolism, membrane and transportation, signal transduction, other metabolic processes, and unknown biological processes. Nine proteins were simultaneously presented in both roots and leaves exposed to drought-cold stress, and the majority of proteins identified differed from one another and displayed differently altered abundance. These findings uncovered organ-specific differences in adaptation to drought-cold stress. Exogenous abscisic acid (ABA) application conferred the plant with protection against drought-cold stress and significantly increased catalase and peroxidase enzyme activities, as well as the transcription of glutathione S-transferase and other 11 sample genes in the roots or leaves, respectively. These results suggested that ABA is a potentially vital factor that contributes to the drought-cold signaling pathway and a promising target for growth recovery. Furthermore, VIGS (virus-induced gene silencing)-treated plants generated for three candidate protein genes TaGRP2, CDCP and WCOR410c were subjected to drought-cold limitation, they showed more serious droop and wilt, increased rate of relative electrolyte leakage, and reduced relative water content (RWC) compared to viral control plants. These results may indicate that TaGRP2, CDCP and WCOR410c play important roles in conferring drought-cold tolerance in wheat. These findings can provide useful insights into the molecular mechanisms of drought-cold responses in higher plants.
2018-05-17 | PXD004396 | Pride
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
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.
2012-01-01 | GSE31639 | GEO
Project description:To undersand the machanism underlying the drought and cold srress tolerance of Ammopiptanthus mongolicus,we investigate the gene expression profile of Ammopiptanthus mongolicus leaves under drought stress(1hours,24hours,72hours) and low temperature (1hours,72hours ).
2016-01-21 | GSE54251 | GEO
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
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
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
Project description:<p><em>Cryptomeria fortunei</em> 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) <em>C. fortunei</em> 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 <em>C. fortunei,</em> and our results provide an excellent foundation for the molecular mechanism of <em>C. fortunei</em> in response to cold stress.</p>
2022-08-12 | MTBLS3184 | MetaboLights
Project description:We applied the tiling arrays to study the Arabidopsis whole-genome transcriptome under drought, cold, high-salinity and ABA treatment conditions and idenfied many stress- or ABA- responsive putative functional RNAs and fully-overlapping sense-antisense transcripts in Arabidopsis genome. Keywords: stress response
2008-11-19 | GSE9646 | GEO