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POWERDERESS and HDA9 interact and promote histone H3 deacetylation at specific lysine residues in Arabidopsis. [RNA-Seq]

ABSTRACT: 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.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE89769 | GEO | 2017/01/25

SECONDARY ACCESSION(S): PRJNA353122

REPOSITORIES: GEO

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POWERDERESS and HDA9 interact and promote histone H3 deacetylation at specific lysine residues in Arabidopsis. [ChIP-Seq]

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

Genome-wide anaylsis of histone acetylation during mouse ESC differentiation [ChIP-seq]

Project description:Using acetylated histone H3 ChIP-seq, we reveal that the histone H3 acetylation level is gradually increased on the neural gene loci while decreased on the neural-inhibitory gene loci during mouse ESC neural differentiation. By overlapping with the targets of HDAC1 ChIP-seq, we identify Nodal as a target gene repressed by histone deacetylation. Thus, our study reveals an intrinsic mechanism that epigenetic histone deacetylation ensures neural fate commitment by restricting Nodal signaling. Examination of HDAC1 in differentiated day 2 cells and acetylated histone H3 in day 2, day 4 and day 6 cells.

2015-02-19 | E-GEOD-66025 | biostudies-arrayexpress

Powerdress Mediated Histone Deacetylation Is Essential For Thermomorphogenesis In Arabidopsis Thaliana

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.

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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

Expression data from wild type versus HDAC knock out mouse embryonic stem cells

Project description:Histone deacetylase 1 (HDAC1) is an enzyme that promotes deacetylation of acetylated lysine residues in histones and other proteins. Histone acetylation is often associated with gene activation and expression. Los of HDAC1 leads to severe problems in development and proliferation. Moreover, it seems to be the major histone deacetylase in mouse embryonic stem cells. We used microarrays to identify putative HDAC1 target genes. Keywords: Fold change anaylsis between wild type nad HDAC KO ES cells

2006-09-19 | GSE5583 | GEO

Vascular histone deacetylation by pharmacological HDAC inhibition [TSA, ChIP-seq]

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

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2014-02-23 | E-GEOD-54909 | biostudies-arrayexpress

Vascular histone deacetylation by pharmacological HDAC inhibition [TSA, RNA-seq]

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 mRNA profiles of TSA treated and control samples were generated by deep sequencing, in triplicate, using Illumina GAIIx.

2014-02-23 | E-GEOD-37376 | biostudies-arrayexpress

Vascular histone deacetylation by pharmacological HDAC inhibition

Project description:This SuperSeries is composed of the SubSeries listed below. 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. Refer to individual Series

2014-02-23 | E-GEOD-37378 | biostudies-arrayexpress

Vascular histone deacetylation by pharmacological HDAC inhibition [SAHA, RNA-seq]

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 mRNA profiles of SAHA treated and control samples were generated by deep sequencing, in triplicate, using Illumina GAIIx.

2014-02-23 | E-GEOD-54912 | biostudies-arrayexpress

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