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Jasmonates and Histone deacetylase 6 activate Arabidopsis genome-wide histone acetylation and methylation during the early acute stress response

ABSTRACT: Jasmonates and Histone deacetylase 6 activate Arabidopsis genome-wide histone acetylation and methylation during the early acute stress response

PROVIDER: PRJNA683647 | ENA |

REPOSITORIES: ENA

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Jasmonates and Histone deacetylase 6 activate Arabidopsis genome-wide histone acetylation and methylation during the early acute stress response

Project description:Jasmonates and Histone deacetylase 6 activate Arabidopsis genome-wide histone acetylation and methylation during the early acute stress response

| PRJNA811774 | ENA

Jasmonates and Histone deacetylase 6 activate Arabidopsis genome-wide histone acetylation and methylation during the early acute stress response.

Project description:BackgroundJasmonates (JAs) mediate trade-off between responses to both biotic and abiotic stress and growth in plants. The Arabidopsis thaliana HISTONE DEACETYLASE 6 is part of the CORONATINE INSENSITIVE1 receptor complex, co-repressing the HDA6/COI1-dependent acetic acid-JA pathway that confers plant drought tolerance. The decrease in HDA6 binding to target DNA mirrors histone H4 acetylation (H4Ac) changes during JA-mediated drought response, and mutations in HDA6 also cause depletion in the constitutive repressive marker H3 lysine 27 trimethylation (H3K27me3). However, the genome-wide effect of HDA6 on H4Ac and much of the impact of JAs on histone modifications and chromatin remodelling remain elusive.ResultsWe performed high-throughput ChIP-Seq on the HDA6 mutant, axe1-5, and wild-type plants with or without methyl jasmonate (MeJA) treatment to assess changes in active H4ac and repressive H3K27me3 histone markers. Transcriptional regulation was investigated in parallel by microarray analysis in the same conditions. MeJA- and HDA6-dependent histone modifications on genes for specialized metabolism; linolenic acid and phenylpropanoid pathways; and abiotic and biotic stress responses were identified. H4ac and H3K27me3 enrichment also differentially affects JAs and HDA6-mediated genome integrity and gene regulatory networks, substantiating the role of HDA6 interacting with specific families of transposable elements in planta and highlighting further specificity of action as well as novel targets of HDA6 in the context of JA signalling for abiotic and biotic stress responses.ConclusionsThe findings demonstrate functional overlap for MeJA and HDA6 in tuning plant developmental plasticity and response to stress at the histone modification level. MeJA and HDA6, nonetheless, maintain distinct activities on histone modifications to modulate genetic variability and to allow adaptation to environmental challenges.

| S-EPMC8996529 | biostudies-literature

Jasmonates and Histone deacetylase 6 activate Arabidopsis genome-wide histone acetylation and methylation during the early acute stress response

Project description:To analyze the extent of the overlap between MeJA-induced transcripts and MeJA- induced histone acetylation, the expression profiles of WT untreated (WT), WT+MeJA, axe1-5 untreated and axe1-5+MeJA samples were analysed using the catalog microarray (Agilent design ID:21169). Whole A. thaliana seedlings of axe1-5 mutant and DR5 wild-type lines (Murfett et al 2001) were grown in vitro for 12 days on 1% Murashige and Skoog (MS) medium (Duchefa) supplemented with 1% sucrose, 0.8% phytoagar (Duchefa) and buffered to pH 5.8. Stratification of seeds was performed for 3 days at 4°C in the dark. Seeds were then grown with plates approximately 20° to vertical under 16h light/8h dark cycles for 12 days at 22°C and a light intensity of 100-120 µmol m-2s-1. Twelve-day-old in vitro grown whole seedlings were transferred to 50 µM MeJA or mock plates and sampled after 3 hours for microarray analysis. Expression profiles were analyzed using the catalog microarray (Agilent design ID:21169).

2022-04-11 | GSE162891 | GEO

Histone deacetylase 1 (HDAC1) complexes regulate both histone acetylation and crotonylation in vivo

Project description:Histone deacetylase 1 (HDAC1) complexes regulate both histone acetylation and crotonylation in vivo

| PRJNA476798 | ENA

Jasmonates and Histone deacetylase 6 activate Arabidopsis genome-wide histone acetylation and methylation during the early acute stress response

Project description:We report the application of ChIP-Seq of H4ac and H3K27me3 histone modifications to jasmonate-treated wild type (DR5) and HDA6 mutant (axe1-5) whole A. thaliana seedlings

2022-04-11 | GSE197733 | GEO

Specific acetylase-deacetylase balance controls stress adaptation by modulating global histone H3K14 acetylation.

Project description:Histone acetylation and deacetylation is important for gene regulation. The histone acetyltransferase, Gcn5, is a known activator of transcriptional initiation that is recruited to gene promoters. Here we map genome-wide levels of Gcn5 occupancy and histone H3K14ac at high resolution. Gcn5 is predominantly localized to coding regions of highly transcribed genes where it antagonistically collaborates with the class II histone deacetylase, Clr3, to regulate histone H3K14ac levels. Regulation of histone H3k14ac levels is critical for regulation of many genes during stress adaptation. Our findings suggest a novel role for Gcn5 during transcriptional elongation in addition to its known role in transcriptional initiation. The data in this series showed Gcn5 occupancy and H3K14 acetylation levels in wild type, gcn5- and gcn5-/clr3- cells under KCl stress condition. Related expression data are GSE5227 and GSE13817 Keywords: Chip-chip

2009-08-01 | GSE13790 | GEO

MAPK-triggered chromatin reprogramming by histone deacetylase in plant innate immunity

Project description:Microbial-associated molecular patterns (MAMPs) activate several MAP Kinases (MAPKs), which are major regulators of the innate immune response in Arabidopsis that induce large-scale changes in gene expression. Here, we determined whether MAMP-triggered gene expression involves chromatin modifications at the chromosomal level. Our results show that histone acetylation and deacetylation are major regulators of MAMP-triggered gene expression and implicate the histone deacetylase HD2B in the reprogramming of defense gene expression and innate immunity. The MAPK MPK3 directly interacts with and phosphorylates HD2B, thereby regulating the intra-nuclear compartmentalization and function of the histone deacetylase. By studying a number of gene loci that undergo MAMP-dependent activation or repression, our data reveal a mechanistic model for how protein kinase signaling directly impacts chromatin reprogramming in plant defense.

2017-06-13 | GSE99936 | GEO

Transcriptional response to histone deacetylase inhibitors

Project description:Histone deacetylase inhibitors are a class of drug which rapidly induce hyperacetylation of histone proteins. Here, we aimed to study the association between HDACi-induced histone acetylation and changes in gene expression. To study the early responses to HDACi treatment we treated cells with three different concentrations of two HDACi, sodium valproate (VPA) and suberoylanilide hydroxamic acid over a short timecourse.

2015-08-31 | GSE65297 | GEO

Proteome-wide lysine acetylation profiling to investigate the involvement of histone deacetylase HDA5 in the salt stress response of Arabidopsis leaves

Project description:Post-translational modifications (PTMs) of proteins play important roles in the acclimation of plants to environmental stress. Lysine acetylation is a dynamic and reversible PTM, which can be removed by histone deacetylases. Here we investigated the role of lysine acetylation in the response of Arabidopsis leaves to one week of salt stress. A quantitative mass spectrometry analysis revealed an increase in lysine acetylation of several proteins from cytosol and plastids, which was accompanied by an altered HDAC activity in the salt-treated leaves. While activities of HDA14 and HDA15 were decreased upon salt stress, HDA5 showed a mild and HDA19 a strongly increased activity. Since HDA5 is a cytosolic-nuclear enzyme from the class II histone deacetylase family with yet unknown protein substrates, we performed a lysine acetylome analysis on hda5 mutants and characterized its substrate proteins. Next to histone H2B, the salt stress responsive transcription factor GT2L and the dehydration-related protein ERD7 were identified as HDA5 substrates. In addition, in protein-protein interaction studies HDA18 was discovered, among other interacting proteins, to work in a complex together with HDA5. Altogether this study revealed the substrate proteins of HDA5 and identified new lysine acetylation sites which are hyperacetylated upon salt stress. The identification of the specific histone deacetylase substrate proteins, apart from histones, will be important to unravel the acclimation response of Arabidopsis to salt stress and their role in plant physiology.

2023-03-28 | PXD032867 | JPOST Repository

Development of miRNA expression signatures for induction of histone deacetylase inhibitor (part 2)

Project description:To clarify the relationship between histone acetylation and miRNA expression, we performed miRNA arrays to detect histone deacetylase inhibitor (OBP-801) induced miRNA regulating AR expression in 22Rv1. Agilent-031181 Unrestricted Human miRNA Microarray (Agilent Technologies, Santa Clara, California) was used according to the manufacturerâs protocols.

2016-06-01 | E-GEOD-69488 | biostudies-arrayexpress

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