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

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 related data for this are GSE13790 and GSE5227

ORGANISM(S): Schizosaccharomyces pombe

PROVIDER: GSE13817 | GEO | 2009/08/01

SECONDARY ACCESSION(S): PRJNA110591

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

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

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

Gcn5 and Esa1 function as histone crotonyltransferases to regulate crotonylation-dependent transcription

Project description:Histone post-translational modifications (PTMs) are critical for processes such as transcription. The more notable among these are the non-acetyl histone lysine acylation modifications such as crotonylation, butyrylation and succinylation. However, the biological relevance of these PTMs is not fully understood because their regulation is largely unknown. Here, we set out to investigate whether the main histone acetyltransferases in budding yeast, Gcn5 and Esa1, possess crotonyltransferase activity. In vitro studies revealed that the Gcn5-Ada2-Ada3 (ADA) and Esa1-Yng2-Epl1 (Piccolo NuA4) histone acetyltransferase complexes have the capacity to crotonylate histones. Mass spectrometry analysis revealed that ADA and Piccolo NuA4 crotonylate lysines in the N-terminal tails of histone H3 and H4, respectively. Functionally, we show that crotonylation selectively affects gene transcription in vivo in a manner dependent on Gcn5 and Esa1. Thus, we identify the Gcn5- and Esa1-containing ADA and Piccolo NuA4 complexes as bona fide crotonyltransferases that promote crotonylation-dependent transcription.

2019-11-06 | PXD015488 | Pride

PCAF/GCN5-regulated genes in MEFs

Project description:Histone acetyltransferases (HATs) GCN5/PCAF and CBP/p300 are transcription coactivators. However, how these HATs regulate ligand-induced nuclear receptor target gene expression remains unclear. Here we show in mouse embryonic fibroblasts (MEFs), deletion of GCN5/PCAF specifically eliminates acetylation on H3K9 (H3K9Ac) while deletion of CBP/p300 selectively reduces acetylation on H3K18 and H3K27 (H3K18/27Ac). Treating MEFs with a specific ligand for nuclear receptor PPARdelta induces sequential increases of H3K18/27Ac and H3K9Ac on the promoter of PPARdelta target gene Angptl4, which correlates with a robust ligand-induced Angptl4 expression. Inhibiting transcription elongation blocks ligand-induced H3K9Ac but not H3K18/27Ac on Angptl4 promoter. Finally, we show CBP/p300 and their HAT activities are required, while GCN5/PCAF and H3K9Ac are dispensable, for ligand-induced PPARdelta target gene expression in MEFs. These results highlight the substrate and site specificities of HATs in cells, and suggest that GCN5/PCAF- and CBP/p300-mediated histone acetylations play distinct roles in regulating ligand-induced nuclear receptor target gene expression. PCAF and GCN5 have some redundant function. To identify PCAF/GCN5-regulated genes, immortalized MEFs with PCAF knockout and GCN5 conditional knockout were infected with retroviruses expressing either Cre recombinase or vector alone. We prepared duplicated RNAs from either vector or Cre infected cells (PCAF-/-;GCN5+/- or PCAF-/-;GCN5+/-) and RNAs from either Vector or Cre infected the other independently immortalized cells for 6 affymetrix microarray.

2013-12-31 | E-GEOD-20008 | biostudies-arrayexpress

Chromatin immunoprecipitation of GCN5 target sites in Arabidopsis gcn5 mutant and wild type seedlings

Project description:GCN5 plays an essential role in chromatin modification and transcriptional regulation, its mode of action is not understood. It is therefore crucial to determine what are the sites targeted by GCN5 in the Arabidopsis genome to decipher the regulatory mechanisms in which it is involved. Array technologies have been used in recent years to determine, at the scale of whole genomes, the sites bound in vivo by chromatin-associated proteins (Hanlon and Lieb 2004) or targeted by chromatin-modifying enzymes (Millar and Grunstein 2006; Zhang et al. 2006). In this study we took advantage of the chromatin immunoprecipitation (ChIP) technique coupled with hybridization to a novel Arabidopsis promoter array to show that GCN5 is recruited to a large number of transcriptionally active promoters.

2007-10-01 | E-MEXP-1233 | biostudies-arrayexpress

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

Conserved and plant-specific GCN5-containing complexes cooperate to regulate gene transcription and plant development [30d RNA-seq]

Project description:Although a conserved SAGA complex containing the histone acetyltransferase GCN5 is known to mediate histone acetylation and transcriptional activation in eukaryotes, how to maintain different levels of histone acetylation and transcription at the whole-genome level remains to be determined. Here, we identify and characterize a plant-specific GCN5-containing complex, which we term PAGA, in Arabidopsis thaliana and Oryzae sativa. In Arabidopsis, the PAGA complex consists of two conserved subunits (GCN5 and ADA2A) and four plant-specific subunits (SPC, ING1, SDRL, and EAF6). Chromatin immunoprecipitation and sequencing indicate that PAGA and SAGA have both shared and specific target genes, and independently mediate moderate and high levels of histone acetylation, thereby promoting moderately and highly transcriptional activation, respectively. By combining RNA-seq and ChIP-seq data, we found that PAGA and SAGA antagonistically regulate histone acetylation and gene transcription. Genetically, PAGA mutations can partially rescue the developmental defects of the SAGA-specific mutant ada2b-c. Unlike SAGA, which regulates multiple biological processes, PAGA is specifically involved in plant height and branch growth by regulating the transcription of hormone biosynthesis and response related genes. These results reveal how PAGA and SAGA cooperate to regulate histone acetylation, transcription, and development. Given that the PAGA mutants show semi-dwarf and increased branching phenotypes without reduction in seed yield, the PAGA mutations could potentially be used for crop improvement.

2023-01-09 | GSE217485 | GEO

Conserved and plant-specific GCN5-containing complexes cooperate to regulate gene transcription and plant development [H3K14Ac ChIP-seq]

2023-01-09 | GSE217476 | GEO

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

2013-07-22 | GSE36600 | GEO