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

ABSTRACT: 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

ORGANISM(S): Schizosaccharomyces pombe

PROVIDER: GSE13790 | GEO | 2009/08/01

SECONDARY ACCESSION(S): PRJNA110545

REPOSITORIES: GEO

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Deletion of Clr3 restores expression of a subset of genes in gcn5- mutant cells

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 related data for this are GSE13790 and GSE5227 Data showed expression pattern of gcn5- vs gcn5-clr3- and clr3- vs wild type under KCl stress in S. pombe. Two biological replicates are used with dye-swap labeling.

2010-06-24 | E-GEOD-13817 | biostudies-arrayexpress

Deletion of Clr3 restores expression of a subset of genes in gcn5- mutant cells

2009-08-01 | GSE13817 | GEO

Histone H3K9 and H3K14 acetylation mark active enhancers and promoters together with bivalent promoters in mouse embryonic stem cells

Project description:Transcription regulation in pluripotent embryonic stem (ES) cells is a complex process that involves multitude of regulatory layers, one of which is post-translational modification of histones. Here we have investigated the genome-wide occurrence of two histone marks, acetylation of histone H3K9 and K14 (H3K9ac and H3K14ac), in mouse ES cells. We demonstrate genome-wide that H3K9ac and H3K14ac show very high correlation. Examination of H3K9ac and H3K14ac in mES cells

2012-10-01 | E-GEOD-31284 | biostudies-arrayexpress

GCN5 modulates salicylic acid homeostasis by regulating H3K14ac levels at the 5ʹ and 3ʹ ends of its target genes

Project description:The modification of histones by acetyl groups has a key role in the regulation of chromatin structure and transcription. The Arabidopsis thaliana histone acetyltransferase GCN5 regulates histone modifications as part of the Spt-Ada-Gcn5 Acetyltransferase (SAGA) transcriptional coactivator complex. GCN5 was previously shown to acetylate lysine 14 of histone 3 (H3K14ac) in the promoter regions of its target genes; however, its binding did not systematically correlate with gene activation and the mechanism by which GCN5 controls transcription thus remained unclear. To gain insight into GCN5 function, we fine-mapped its genome-wide binding sites and explored the effect of GCN5 loss-of-function on the expression of its target genes, finding that GCN5 has a dual role in the regulation of H3K14ac levels in their 5ʹ and 3ʹ ends. We found that the gcn5 mutation leads to a genome-wide reduction of H3K14ac in the 5ʹ end of some of the GCN5 targets, a phenomenon associated to their down-regulated in the gcn5 mutant. By contrast, an increase of H3K14ac in the 3ʹ end was observed in GCN5 targets that are up-regulated in the gcn5 mutant, indicating that this protein plays a dual role in the control of H3K14ac levels and in the regulation of transcription. Furthermore, changes in H3K14ac levels in the gcn5 mutant correlated with changes in H3K9ac in a genome-wide fashion at both 5ʹ and 3ʹ ends, providing evidence for a molecular link between the deposition of these two histone modifications. Finally, we show that GCN5 participates in responses to biotic stress by repressing salicylic acid (SA) accumulation and SA-mediated immunity, highlighting the role of this protein in the regulation of the crosstalk between diverse developmental and stress-responsive physiological programs.

2020-04-28 | GSE137474 | GEO

Histone H3K9 and H3K14 acetylation mark active enhancers and promoters together with bivalent promoters in mouse embryonic stem cells

2012-10-01 | GSE31284 | GEO

EIN2 mediates histone H3K14 and non-canonical histone H3K23 acetylation in the nucleus in ethylene response [ChIP-seq]

Project description:We report that ethylene specifically elevated acetylation of histone H3 at K14 and the non-canonical acetylation of histone H3 at K23. We perform Chip-sequencing of H3K14Ac, H3K23Ac and H3K9Ac using chromatins isolated from 3-day old etiolated Col-0 seedlings treated with ethylene or air gas. Results show that ethylene specifically elevates H3K14Ac and non-canonical H3K23Ac in EIN3 targeted genes that are regulated at the transcriptional level by ethylene.

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Stem cell plasticity, acetylation of H3K14 and de novo gene activation rely on KAT7

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2022-12-09 | GSE220602 | GEO

H3K36Ac ChIP chips

Project description:Histone lysine (K) acetylation is a major mechanism by which cells regulate the structure and function of chromatin, and new sites of acetylation continue to be discovered. Here we identify and characterize histone H3K36 acetylation (H3K36ac). By mass spectrometric analysis of H3 purified from Tetrahymena thermophila and S. cerevisiae (yeast), we find that H3K36 is acetylated in addition to being methylated. Using an antibody specific to H3K36ac, we show that this modification is conserved in mammals. In yeast, genome-wide ChIP-chip experiments show that H3K36ac is localized predominantly to the promoters of RNA polymerase II-transcribed genes, a pattern mutually exclusive to that of H3K36 methylation. The pattern of H3K36ac localization is similar to that of other sites of H3 acetylation, including H3K9ac and H3K14ac. Using histone acetyltransferase complexes purified from yeast, we show that the Gcn5-containing SAGA complex specifically acetylates H3K36 in vitro. Deletion of GCN5 completely abolishes H3K36ac in vivo. The regulation of H3K36ac by Gcn5 suggests a function for this modification in transcription. These data expand our knowledge of the genomic targets of Gcn5, show H3K36ac is highly conserved, and raise the intriguing possibility that the transition between H3K36ac and H3K36me acts as a switch in chromatin function along transcription units. This SuperSeries is composed of the SubSeries listed below.

2006-11-01 | GSE5544 | GEO

Chromatin immunoprecipitation and high-throughput sequencing (ChIP-seq) detection of histone H3 lysine 14 acetylation (H3K14ac) and KAT7 (HBO1) in E14.5 mouse neural stem and progenitor cells (NSPCs)

Project description:Tissue specific deletion of the gene encoding the histone acetyltransferase KAT7 (HBO1) in the developing mouse central nervous system using cre-recombinase expression driven by regulatory sequences of the nestin locus (NesCre transgene) resulted in defective cerebral cortex development, a complete failure of neural stem cells to give rise to neurons and oligodendrocytes during in vitro differentiation and a failure to express the neuronal differentiation program. KAT7 genome occupancy and histone H3 lysine 14 acetylation (H3K14ac) levels were assessed by ChIP-seq in proliferating Kat7 deleted vs. Kat7 intact neural stem and progenitor cells (NSPCs). KAT7 and H3K14ac were completely absent in the Kat7 deleted cells. IN KAT7 intact cells, KAT7 occupancy levels and H3K14ac levels within the body of genes correlated strongly and positively. Both were higher in genes that were expressed strongly than in genes with lower or no expression. However, KAT7 and H3K14ac were present in all genes including silent genes and in all other regions of the genome, including intergenic regions and regions decorated with histone H3 lysine 9 trimethylation (H3K9me3), an indicator of constitutive heterochromatin.

2022-11-30 | GSE216459 | GEO

Genome-wide enrichment of Gcn5 and H3K18/H4K16 acetylation under physiological change of stress adaptation and stress recovery

Project description:The data provide information of Gcn5 enrichment, H3K18 and H4K16 acetylation level and Histone H3 density for 5 different physioloigcal conditions during stress adpatation and stress recovery (normal growth, during stress adaptation, after stress adaptation, under stress recovery, after stress recovery) in yeast. The purpose of the study is to understand how histone acetyltransferase HATs (Gcn5) apply it is function in gene regulation by changing global or local histone acetylation level under different physiological conditions. Gcn5 enrichment, H3K18 and H4K16 acetylation level and Histone H3 density are mearured and compared to input signal for 5 different physioloigcal conditions (normal growth, during stress adaptation, after stress adaptation, under stress recovery, after stress recovery). Replicates are used.

2013-07-22 | E-GEOD-36600 | biostudies-arrayexpress

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