The role of H3K4me3 of low temperature memory in Arabidopsis [ChIP-Seq]
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ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE212784 | GEO | 2022/09/11
REPOSITORIES: GEO
Similar Datasets
Project description:Plants experience a wide array of environmental stimuli to form a memory of adversity. Histone modification plays roles in plant stress memory, of which the mechanisms of H3K4me3 of low temperature memory in plants are poorly understood although H3K4me3 is a key histone modification. Combined with phenotypic analysis, chip-seq, and transcriptome analyses were performed to investigate the potential H3K4me3 contributions for different phases of recurring cold stresses Arabidopsis plants. We then performed gene expression profiling analysis using data obtained from RNA-seq of different low temperature treatments.
2023-09-01 | GSE217609 | GEO
Project description:Vernalization, the requirement of long-term exposure to low environmental temperature for flowering, is a typical epigenetic phenomenon in plants. Histone modifications have been analyzed for key vernalization genes, but genome-wide regulation remains unclear. Here, we performed global analysis of histone 3 lysine 4 (H3K4me3) and 27 (H3K27me3) trimethylation with Chromatin Immunoprecipitation-Sequencing (ChIP-Seq) during and after vernalization to obtain complete view of histone modification fluctuation both on whole genome scale and for single genes, even different regions of genes. The critical role of H3K27me3 was revealed. During vernalization H3K27me3 regulation concentrated on a few biological processes, with two essential environmental responses, transcription regulation and anti-stress reactions, being main targets, as indicated by change pattern and GO analysis. The regulation of H3K4me3, however, showed no obvious focus. For gene expression, H3K27me3 is involved in multiple trends of control. H3K4me3, however, mainly focuses on unidirectional regulation. After vernalization most of H3K27me3 changes were kept, but relatively small proportion of H3K4me3 changes could be maintained, as shown by multiple-level analysis, suggesting the active role of H3K27me3 in epigenetic memory. Vernalization-induced histone modification changes were uncovered for VRN3, a gene integrating vernalization/photoperiod signals, suggesting its regulation role at epigenetic level. Memory-related genes were genome-widely identified and a high proportion of them showed quantitative response to vernalization-treatment, suggesting broad existence of this mechanism. Our studies shed new light on epigenetic role of H3K27me3 and VRN3 in vernalization, revealed mechanism underlying epigenetic memory, which helps us to further understand vernalization, a mechanism with great potential in agriculture.
2018-05-22 | GSE93140 | GEO
Project description:Plants can be primed by a stress cue to mount a faster and stronger activation of defense mechanisms upon a subsequent stress. A crucial component of such stress priming is the modified reactivation of genes upon recurring stress, a phenomenon known as transcriptional memory. The transcriptional memory in response to heat stress is not clear at the genome scale. We used microarrays to identify genes that showed transcriptional memory in response to recurring heat stress.
2018-07-09 | GSE103398 | GEO
Project description:A role of chromatin in plant memory of environmental stress has been proposed. In this study ChIP-Seq was employed to investigate whether a transient mild salt treatment of Arabidopsis thaliana plant at seedling stage (M-^Qpriming treatmentM-^R: 50 mM NaCl for 24 hours) altered genome-wide profiles of four histone modifications; H3K4me2, H3K4me3, H3K9me2 and H3K27me3. Comparison of histone modification profiles between primed and non-primed plants harvested immediately after the priming treatment showed differences in all histone modifications but were strongest and most abundant for H3K27me3. We subsequently explored whether these changes were maintained over an extensive period of growth in control conditions. Additional ChIP-Seq analysis showed that differences in the H3K27me3 profiles between primed and non-primed plants were still apparent after a growth period of ten days in control conditions. The results provide first indication for a potential role of H3K27me3 in long-term somatic memory of abiotic stress events in plants. The obtained dataset was compared with RNA-seq data measured in the same plant material (see parallel submission of RNA-Seq data in ArrayExpress: https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1668).
2013-06-01 | E-MTAB-1663 | biostudies-arrayexpress
Project description:Plants often experience recurrent stressful events, for example during heat waves. They can adapt to such recurrent heat stress (HS), allowing subsequent survival of more severe HS conditions. At certain genes HS induces sustained expression for several days beyond the actual HS. This transcriptional memory is associated with hyper-methylation of histone H3 lysine 4 (H3K4me3), however, how this is maintained for extended periods of time is unclear. Here, we determined histone turnover by measuring chromatin association of a HS-induced histone H3.3. Genome-wide Histone turnover was not homogenous, in particular, H3.3 was retained longer at HS memory genes compared to HS-induced non-memory genes during the memory phase. While low nucleosome turnover retained H3K4 methylation, its loss did not affect turnover, suggesting that low nucleosome turnover sustains H3K4 methylation (and not vice versa). Together, our results unveil the modulation of histone turnover as a mechanism to retain environmentally-mediated epigenetic modifications.
2023-10-18 | GSE218234 | GEO
Project description:In response to environmental stressors, plants exhibit a phenomenon known as stress memory, whereby a prior stress episode influences their subsequent responses. This suggests the existence of a molecular memory mechanism that allows plants to adapt to recurring stress events. Previous work has highlighted the contribution of the phytohormone strigolactones to drought stress and memory thereof (10.1007/s00425-015-2266-8; 10.1111/nph.14190; 10.1111/pce.13758; 10.1093/pcp/pcac058). Additionally, there are sparse indications that especially (but not only) in Solanaceous plants, they may have a significant effect on reproduction (reviewed by 10.1111/pce.14461). However, the molecular underpinnings of both phenomena have not been researched yet. This study investigated the positioning of strigolactones to the tomato flowering network, and their contribution to drought memory.
2024-04-17 | GSE264066 | GEO
Project description:In nature, plants are often exposed to recurring adverse environmental conditions. Acclimation to high temperature stress entails transcriptional responses that are mediated by heat-shock transcription factors (HSFs), and they are primed to better withstand subsequent stress events. This heat stress (HS)-induced transcriptional memory results in more efficient re-induction of transcription upon recurring HS. However, the mechanisms by which HSFs recruit and enact the transcriptional machinery remain unclear. Here, we identified two subunits of the kinase module of the Mediator transcriptional co-regulator complex, CDK8 and MED12, as regulators of HS memory in Arabidopsis thaliana. Enhanced re-induction of gene expression after recurrent HS and physiological HS memory, as well as H3K4 methylation are compromised in cdk8 and med12 mutants. HSFA2 interacts with CDK8 during and after HS and recruits it to memory gene loci, where CDK8 binds in the promoter but also the gene body, together with core Mediator and RNA polymerase II (Pol II). Our data suggest that CDK8 resolves stalled Pol II complexes or promotes efficient recycling for subsequent cycles of transcription. As HSFA2, CDK8 is largely dispensable for the initial induction of gene expression after HS and thus promotes transcriptional memory independently of HS-dependent primary gene induction. Our findings provide a model for the complex role of the Mediator kinase module during transcriptional memory in multicellular eukaryotes through interaction with transcription factors, chromatin modifications and promotion of Pol II productivity.
2023-12-12 | GSE232094 | GEO
Project description:Arabidopsis plants that have experienced stress from water withdrawal show an improved ability to tolerate subsequent exposures as a ‘memory’ from the previous stress. This physiological stress memory is associated with ‘transcriptional memory’ illustrated by a subset of dehydrations stress responding genes that produce significantly different transcript amounts during repeated dehydration stresses relative to their response in the first. Here we report the genome-wide representation of dehydration stress transcriptional memory genes in A. thaliana. We identify four novel transcription patterns in response to repeated dehydration stress treatments. The nature of the proteins encoded by genes from each type of memory-response pattern is analyzed and the consequences of the genes’ memory behavior are considered in the context of possible biological relevance. The memory behavior of genes co-regulated by the dehydration/ABA and other abiotic stress and hormone responding pathways suggested that the crosstalk at the transcriptional level between them was affected as well. The intensity and the nature of specific biochemical, membrane, chloroplast, and stress response-related interactions during multiple exposures to dehydration stress are different from the responses to a single dehydration stress. The results reveal additional, hitherto unknown, levels of complexity of the plants’ transcriptional behavior when adjusting and adapting to recurring water deficits. For each condition (water, S1, and S3) the transcriptome was sequenced for two replicates. The watered condition is considered the control.
2014-01-01 | E-GEOD-48235 | biostudies-arrayexpress
Project description:Arabidopsis plants that have experienced stress from water withdrawal show an improved ability to tolerate subsequent exposures as a ‘memory’ from the previous stress. This physiological stress memory is associated with ‘transcriptional memory’ illustrated by a subset of dehydrations stress responding genes that produce significantly different transcript amounts during repeated dehydration stresses relative to their response in the first. Here we report the genome-wide representation of dehydration stress transcriptional memory genes in A. thaliana. We identify four novel transcription patterns in response to repeated dehydration stress treatments. The nature of the proteins encoded by genes from each type of memory-response pattern is analyzed and the consequences of the genes’ memory behavior are considered in the context of possible biological relevance. The memory behavior of genes co-regulated by the dehydration/ABA and other abiotic stress and hormone responding pathways suggested that the crosstalk at the transcriptional level between them was affected as well. The intensity and the nature of specific biochemical, membrane, chloroplast, and stress response-related interactions during multiple exposures to dehydration stress are different from the responses to a single dehydration stress. The results reveal additional, hitherto unknown, levels of complexity of the plants’ transcriptional behavior when adjusting and adapting to recurring water deficits.
2014-01-01 | GSE48235 | GEO
Project description:Gene expressions were compared between non-stress Arabidopsis plants (0 hr at low-temperature treatment) and low-temperature treated plants (2 hrs and 10 hrs low-temperature treatment).
2008-05-01 | E-MEXP-761 | biostudies-arrayexpress