Arabidopsis thaliana
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA353121 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR5011160_1.fastq.gz | Fastqsanger.gz | |||
| SRR5011160_2.fastq.gz | Fastqsanger.gz | |||
| SRR5011170.fastq.gz | Fastqsanger.gz | |||
| SRR5011161_1.fastq.gz | Fastqsanger.gz | |||
| SRR5011161_2.fastq.gz | Fastqsanger.gz |
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Project description:POWERDERESS and HDA9 interact and promote histone H3 deacetylation at specific lysine residues in Arabidopsis. [RNA-Seq]
| PRJNA353122 | ENA
Project description:POWERDERESS and HDA9 interact and promote histone H3 deacetylation at specific lysine residues in Arabidopsis.
| PRJNA353120 | ENA
Project description:Histone acetylation is a major epigenetic control mechanism that is tightly linked to the promotion of gene expression. Histone acetylation levels are balanced through the opposing activities of histone acetyltransferases (HATs) and histone deacetylases (HDACs). Arabidopsis HDAC genes (AtHDACs) compose a large gene family, and distinct phenotypes among AtHDAC mutants reflect the functional specificity of individual AtHDACs. However, the mechanisms underlying this functional diversity are largely unknown. Here, we show that POWERDRESS (PWR), a positive regulator of floral stem cell maintenance, interacts with HDA9 and promotes histone H3 deacetylation possibly by facilitating HDA9 function at target chromatin. The PWR SANT2 domain, which is homologous to that of subunits in animal HDAC complexes, showed specific binding affinity to acetylated histone H3. Three lysine residues (K9, K14 and K27) of H3 retained hyperacetylation status in both pwr and hda9 mutants. Genome wide H3K9 and H3K14 acetylation levels were generally elevated, and a large portion of acetylated targets overlapped between the pwr and hda9 mutants. Comparative analysis revealed a correlation between gene expression and histone H3 acetylation status in the pwr and hda9 mutants. In addition, PWR and HDA9 modulated the AGAMOUS-LIKE 19 (AGL19)-mediated flowering time pathway through histone H3 deacetylation. Finally, PWR was shown to physically interact with HDA9. We therefore propose that PWR acts as a subunit in a complex with HDA9 to negatively regulate the acetylation of specific lysine residues of histone H3 at genomic targets.
2017-01-25 | GSE89769 | GEO
Project description:Histone acetylation is a major epigenetic control mechanism that is tightly linked to the promotion of gene expression. Histone acetylation levels are balanced through the opposing activities of histone acetyltransferases (HATs) and histone deacetylases (HDACs). Arabidopsis HDAC genes (AtHDACs) compose a large gene family, and distinct phenotypes among AtHDAC mutants reflect the functional specificity of individual AtHDACs. However, the mechanisms underlying this functional diversity are largely unknown. Here, we show that POWERDRESS (PWR), a positive regulator of floral stem cell maintenance, interacts with HDA9 and promotes histone H3 deacetylation possibly by facilitating HDA9 function at target chromatin. The PWR SANT2 domain, which is homologous to that of subunits in animal HDAC complexes, showed specific binding affinity to acetylated histone H3. Three lysine residues (K9, K14 and K27) of H3 retained hyperacetylation status in both pwr and hda9 mutants. Genome wide H3K9 and H3K14 acetylation levels were generally elevated, and a large portion of acetylated targets overlapped between the pwr and hda9 mutants. Comparative analysis revealed a correlation between gene expression and histone H3 acetylation status in the pwr and hda9 mutants. In addition, PWR and HDA9 modulated the AGAMOUS-LIKE 19 (AGL19)-mediated flowering time pathway through histone H3 deacetylation. Finally, PWR was shown to physically interact with HDA9. We therefore propose that PWR acts as a subunit in a complex with HDA9 to negatively regulate the acetylation of specific lysine residues of histone H3 at genomic targets.
2017-01-25 | GSE89768 | GEO
Project description:We report POWERDRESS (PWR), a SANT domain containing protein known to facilitate the deacetylation of lysine rich residues of histone H3 by HISTONE DEACETYLASE 9 (HDA9), to play key role in temperature induced growth in Arabidopsis thaliana. Mutations in PWR showed severe attenuation in high temperature associated phenotypes viz., temperature-induced hypocotyl elongation, petiole elongation and early flowering. The study involved analysing the impact of the loss of PWR on the transcriptome in response to changes in ambient temperature. About one hundred 6 day old seedlings of wild type (Col-0) and pwr-2 mutant (in Col-0 background) were grown at 23 °C in short days (SD) photoperiod in growth chambers (GR-36, Percival Scientific, Canada). Half of the samples were then shifted to 27°C under short day photoperiod. Total RNA was extracted from whole seedlings grown at 23 °C and 27°C after two hours. Two biological replicates were used for Col-0 and pwr-2 samples. RNA was extracted using Isolate II RNA plant kit (Bioline Pty Ltd, Australia). RNA-Seq libraries were generated on Illumina HiSeqTM 2000 platform using paired-end sequencing of 90 bp in length at BGI-Shenzen (Beijing Genomics Institute). Gene expression analysis was performed using DESeq2 (v1.14.1) differential expression analysis pipeline.
2017-12-01 | GSE101782 | GEO
Project description:Histone 3 lysine 4 and histone 3 lysine 9 methylation in wild type and ddm1 Arabidopsis thaliana seedlings. The purpose of the chromatin immunoprecipitation/microarray (ChIP/chip) experiment is to determine which regions of a genome are enriched for a particular histone modification in a single Arabidopsis thanliana genotype. Chromatin immunoprecipitation with antibodies raised against dimethyl histone-H3 lysine-9 (H3mK9) or dimethyl histone-H3 lysine-4 (H3mK4) is performed on a selected genotype. This purified DNA from each immunoprecipiation (mH3K9, mH3K4, no antibody control) is used for random amplification to increase the quantity of DNA for microarray hybridization. The amplified DNA from each experimental sample is then labeled with Cy5 and hybridized against total input DNA from the corresponding genotype, labeled in Cy3. In a single hybridization, the total input DNA serves as a baseline and is compared to the immunoprecipitated samples. Ratios of normalized signal intensities were calculated to identify enrichment of a particular sequence after immunoprecipitation, in comparison to the total input DNA. Dye swap analysis is carried out to take account of experimental variation by repeating the hybridization with identical samples labeled with Cy3 and Cy5, respectively. This SuperSeries is composed of the following subset Series: GSE1333: EV49+50, Histone 3 Lysine 4 methylation in wild-type Arabidopsis thaliana seedlings GSE1334: Histone 3 Lysine 4 methylation in ddm1 Arabidopsis thaliana seedlings GSE1335: EV104+105, Histone 3 Lysine 4 methylation in ddm1 Arabidopsis thaliana seedlings GSE1336: Ev106+107, Histone 3 Lysine 4 methylation in WT Arabidopsis thaliana seedlings GSE1337: EV51+52, Histone 3 Lysine 9 methylation in wild-type Arabidopsis thaliana seedlings GSE1338: EV59+60, Histone 3 Lysine 9 methylation in ddm1 Arabidopsis thaliana seedlings GSE1339: Histone 3 Lysine 9 methylation in wild-type Arabidopsis thaliana seedlings GSE1340: EV110+111, Histone 3 Lysine 9 methylation in ddm1 Arabidopsis thaliana seedlings Refer to individual Series
2010-06-09 | E-GEOD-1356 | biostudies-arrayexpress
Project description:The objective of the study is to profile histone H3 lysine nine di-methylation (H3K9me2) in Arabidopsis thaliana and to correlate it with DNA methylation.
2008-09-11 | GSE12383 | GEO
Project description:HDAC inhibitors are thought to regulate gene expression by post-translational modification of histone as well as non-histone proteins. Often studied at single loci, increased histone acetylation is the paradigmatic mechanism of action, however, little is known of the extent of genome-wide changes of the mammalian genome when stimulated by the hydroxamic acids, TSA and SAHA. In primary human vascular endothelial cells we map the chromatin modifications, histone H3 acetylation of lysine 9 and 14 (H3K9/14ac) using chromatin immunoprecipitation (ChIP) coupled with massive parallel sequencing (ChIP-seq). Since acetylation mediated gene expression is often associated with modification of other lysine residues we also examined H3K4me3 and H3K9me3 as well as changes in CpG methylation (CpG-seq). Genome-wide mRNA sequencing indicates the differential expression of about 30% of genes, with almost equal numbers being up- and down- regulated. We observe deacetylation conferred by TSA and SAHA that are associated with decreased gene expression. Histone deacetylation is associated with the loss of p300/CBP binding at gene promoters. This study provides an important framework for HDAC inhibitor function in vascular biology and a comprehensive description of genome-wide deacetylation. HAEC ChIP-seq profiles for 3 histone marks of TSA treated and control samples were generated by deep sequencing, in triplicate, using Illumina GAIIx.
2014-02-23 | E-GEOD-37377 | biostudies-arrayexpress
Project description:HDAC inhibitors are thought to regulate gene expression by post-translational modification of histone as well as non-histone proteins. Often studied at single loci, increased histone acetylation is the paradigmatic mechanism of action, however, little is known of the extent of genome-wide changes of the mammalian genome when stimulated by the hydroxamic acids, TSA and SAHA. In primary human vascular endothelial cells we map the chromatin modifications, histone H3 acetylation of lysine 9 and 14 (H3K9/14ac) using chromatin immunoprecipitation (ChIP) coupled with massive parallel sequencing (ChIP-seq). Since acetylation mediated gene expression is often associated with modification of other lysine residues we also examined H3K4me3 and H3K9me3 as well as changes in CpG methylation (CpG-seq). Genome-wide mRNA sequencing indicates the differential expression of about 30% of genes, with almost equal numbers being up- and down- regulated. We observe deacetylation conferred by TSA and SAHA that are associated with decreased gene expression. Histone deacetylation is associated with the loss of p300/CBP binding at gene promoters. This study provides an important framework for HDAC inhibitor function in vascular biology and a comprehensive description of genome-wide deacetylation. HAEC ChIP-seq profiles for 3 histone marks of SAHA treated and control samples were generated by deep sequencing, in triplicate, using Illumina GAIIx.
2014-02-23 | E-GEOD-54909 | biostudies-arrayexpress
Project description:HDAC inhibitors are thought to regulate gene expression by post-translational modification of histone as well as non-histone proteins. Often studied at single loci, increased histone acetylation is the paradigmatic mechanism of action, however, little is known of the extent of genome-wide changes of the mammalian genome when stimulated by the hydroxamic acids, TSA and SAHA. In primary human vascular endothelial cells we map the chromatin modifications, histone H3 acetylation of lysine 9 and 14 (H3K9/14ac) using chromatin immunoprecipitation (ChIP) coupled with massive parallel sequencing (ChIP-seq). Since acetylation mediated gene expression is often associated with modification of other lysine residues we also examined H3K4me3 and H3K9me3 as well as changes in CpG methylation (CpG-seq). Genome-wide mRNA sequencing indicates the differential expression of about 30% of genes, with almost equal numbers being up- and down- regulated. We observe deacetylation conferred by TSA and SAHA that are associated with decreased gene expression. Histone deacetylation is associated with the loss of p300/CBP binding at gene promoters. This study provides an important framework for HDAC inhibitor function in vascular biology and a comprehensive description of genome-wide deacetylation. Mouse ChIP-seq profiles for histone acetylation treated and control samples were generated by deep sequencing, using Illumina GAIIx.
2014-02-23 | E-GEOD-54910 | biostudies-arrayexpress