Salt priming A. thaliana ChIP-Seq
Ontology highlight
ABSTRACT:
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR274502.fastq.gz | Fastqsanger.gz | |||
| ERR274503.fastq.gz | Fastqsanger.gz | |||
| ERR274504.fastq.gz | Fastqsanger.gz | |||
| ERR274505.fastq.gz | Fastqsanger.gz | |||
| ERR274506.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 14 |
Similar Datasets
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:Salt priming A. thaliana RNA-Seq
| PRJEB1937 | ENA
Project description:Estrogen Receptor alpha (ERα) is a key driver of most breast cancers, and it is the target of endocrine therapies used in the clinic to treat women with ERα positive (ER+) breast cancer. The two methods ChIP-seq (chromatin immunoprecipitation coupled with deep sequencing) and RIME (Rapid Immunoprecipitation of Endogenous Proteins) have greatly improved our understanding of ERα function during breast cancer progression and in response to anti-estrogens. A critical component of both ChIP-seq and RIME protocols is the antibody that is used to pull down the bait protein. To date, most of the ChIP-seq and RIME experiments for the study of ERα have been performed using the sc-543 antibody from Santa Cruz Biotechnology. However, this antibody has been discontinued, thereby severely impacting the study of ERα in normal physiology as well as diseases such as breast cancer and ovarian cancer. Here, we compare the sc-543 antibody with other commercially available antibodies, and we show that 06-935 (EMD Millipore) and ab3575 (Abcam) antibodies can successfully replace the sc-543 antibody for ChIP-seq and RIME experiments.
2019-03-21 | PXD012930 | Pride
Project description:CuZn-superoxide dismutase (CuZn-SOD) and ascorbate peroxidase (APX) constitute first line of defence against oxidative stress. In the present study, PaSOD and RaAPX genes from Potentilla atrosanguinea and Rheum australe, respectively were overexpressed individually as well as in combination in Arabidopsis thaliana. We performed RNA-seq analysis of wild type and transgenic Arabidopsis thaliana overexpressing CuZn-SOD, APX and CuZn-SOD + APX under control and salt stress
2014-10-06 | E-MTAB-4434 | biostudies-arrayexpress
Project description:A relationship between transcript level and histone modifications is apparent in steady state but their dynamic relationship remains to be understood. In this study we used RNA-sequencing to determine transcript levels in Arabidopsis thaliana plants after a short, mild salt treatment at seedling stage (ﾓpriming treatmentﾔ: 50 mM NaCl for 24 hours). The obtained dataset was compared with genome-wide histone modification landscapes measured in the same plant material (see parallel submission of ChIP-Seq data in ArrayExpress: https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1663).
2014-05-14 | E-MTAB-1668 | biostudies-arrayexpress
Project description:Arabidopsis thaliana is a glycophyte with a low salt tolerance, while Eutrema is a halophyte with a very high salt tolerance. To elucidate the transcriptional basis of this difference, we performed hydroponis culture experiments where we grew plants under control conditions (25 mM NaCl) or under salt stress (200 mM NaCl for both species, 500 mM for Eutrema). Salt concentration was increased for the stress treatments by increments of 50 mM per day (25 mM on the first day). Plants were grown at the final NaCl concentration for an additional week, when rosettes were harvested for RNA isolation.Expression patterns were compared between treatments and between species.
2016-06-29 | GSE71271 | GEO
Project description:The seed differential proteins of the two varieties were mainly in nucleus, chloroplast and mitochondriaredox. The proteins related to homeostasis, electron transfer activity, photosynthesis and carbohydrate metabolism were significantly affected by salt priming.
2022-03-06 | PXD032090 |
Project description:Purpose: Our previous study has confirmed that reduction of SIRT3 expression is a main factor contributing to salt-induced hepatic inflammtion. Here we sought to investigate whether salt-induced SIRT3 reduction was related to epigenetic modification. Methods: 6-week-old male SIRT3 knockout or their wild-type littermates were fed with high salt diet (HSD, containing 8% NaCl) or normal salt diet (NSD, containing 0.4% NaCl) for 4 months. And then their liver tissues were removed and subjected to ChIP-seq using antibodies against H3K27ac (ab4729), H3K4me1 (ab8895), H3K9ac (39917) and H3 (ab1791). Results: Through ChIP-seq, we observed the enrichment of H3K27ac was increased on the promoters of Sirt3 and some pro-inflammatory genes, including Ccl2, Tnf and Il6, after high salt loading. However, neither H3K4me1 nor H3K9ac displayed such phenomunum. In addition, those genes containing increased H3K27ac level in response to high salt were mainly enriched in metabolism and inflammatory pathways. And knockout of SIRT3 mainly affected genes related to AMP-activated protein kinase (AMPK) and insulin signaling pathways. Conclusions: Salt-induced SIRT3 reduction is related to the epigenetic regulation, especially H3K27ac.
2023-09-01 | GSE183582 | GEO
Project description:Plants must continuously react to the ever-fluctuating nature of their environment. Repeated exposure to stressful conditions can lead to priming, whereby prior encounters heighten a plant’s ability to respond to future events. A clear example of priming is provided by the model plant species Arabidopsis thaliana (Arabidopsis), in which photosynthetic and photoprotective responses are enhanced following recurring light stress. While there are various post-translational mechanisms underpinning photoprotection, an unresolved question is the relative importance of transcriptional changes towards stress priming and, consequently, the potential contribution from DNA methylation – a heritable chemical modification of DNA capable of influencing gene expression. Here, we systematically investigate the potential molecular underpinnings of physiological priming against recurring excess light (EL), specifically DNA methylation and transcriptional regulation: the latter having not been examined with respect to EL priming. The capacity for physiological priming of photosynthetic and photoprotective parameters following a recurring EL treatment was not impaired in Arabidopsis mutants with perturbed establishment, maintenance and removal of DNA methylation, nor was the transmission of this priming into naive tissues developed in the absence of excess light. Importantly, no differences in developmental or basal photoprotective capacity were identified in the mutants that may confound the above result. Little evidence for a causal transcriptional component of physiological priming was identified; in fact, most alterations in primed plants presented as a transcriptional ‘dampening’ in response to an additional EL exposure, likely a consequential of physiological priming. However, a set of transcripts uniquely regulated in primed plants provide preliminary evidence for a novel transcriptional component of recurring EL priming, independent of physiological changes. Thus, we propose that physiological priming of recurring EL in Arabidopsis occurs independently of DNA methylation; and that the majority of the associated transcriptional alterations are a consequence, not cause, of this physiological priming.
2018-11-27 | GSE121150 | GEO
Project description:Salt stress leads to devastating effects to agriculture. Presently, the key regulators that control transcriptional dynamics of salt-responsive genes remain poorly understood in plants. Here, we revealed that salt stress can substantially induce the kinase activity of Mediator subunit cyclin-dependent kinase 8 (CDK8), which is essential for its positive role in regulating salt tolerance. We subsequently uncovered that CDK8 phosphorylates the AT-hook motif nuclear-localized protein 10 (AHL10) at serine 314 through direct interaction, thereby promoting its protein degradation under salt stress. In addition, we created ahl10 mutants by CRISPR-Cas9 and showed the negative role of AHL10 in salt tolerance. Moreover, transcriptome analysis revealed that CDK8 regulates more than 20% of salt-responsive genes, about half of which are co-regulated by AHL10. Chromatin immunoprecipitation sequencing (ChIP-seq) further demonstrated that AHL10 binds to the AT-rich DNA sequence related to the nuclear matrix-attachment regions (MARs) in the salt-responsive gene promoters to repress their transcription. Importantly, we further found that AHL10 physically interacts with SU(VAR)3-9 homologs SUVH2/9, thereby repressing transcription of salt-responsive genes in a H3K9me2-dependent epigenetic regulatory manner. Overall, our study identified the CDK8-AHL10-SUVH2/9 module as a key molecular switch controlling plant transcriptional dynamics in response to salt stress.
2025-02-02 | PXD057837 | JPOST Repository