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

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

PROVIDER: PRJNA899080 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR22220853_1.fastq.gz	Fastqsanger.gz
	SRR22220853_2.fastq.gz	Fastqsanger.gz
	SRR22220854_1.fastq.gz	Fastqsanger.gz
	SRR22220854_2.fastq.gz	Fastqsanger.gz
	SRR22220855_1.fastq.gz	Fastqsanger.gz

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Similar Datasets

Conserved and plant-specific GCN5-containing complexes cooperate to regulate gene transcription and plant development [H3K14Ac ChIP-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 | GSE217476 | GEO

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

2023-01-09 | GSE217485 | GEO

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

Project description:Although the conserved histone acetyltransferase HAG1/GCN5-containing complex SAGA (Spt-Ada-Gcn5 acetyltransferase) has been extensively studied in plants, whether HAG1 forms a plant-specific complex is unknown. Here, we identified a plant-specific GCN5-containing complex, PAGA (plant-ADA2A-GCN5-acetyltransferase), in Arabidopsis thaliana; the complex consists of two conserved subunits (HAG1/GCN5 and ADA2A) and four plant-specific subunits (SPC, ING1, SDRL, and EAF6). In the PAGA complex, SPC functions as a scaffold protein that is responsible for integrating the other subunits. SPC also enhances the binding of ING1 to histone H3 with methylated lysine 4 and promotes the histone acetylation activity of HAG1. Chromatin immunoprecipitation followed by sequencing indicated that PAGA not only shares target genes with SAGA but also has its specific target genes. While PAGA and SAGA promote transcription by mediating moderate and high levels of histone acetylation, respectively, at different sets of genes, PAGA can also function antagonistically against SAGA to prevent excessive transcription of PAGA- and SAGA-shared target genes. Unlike SAGA, which regulates multiple biological processes, PAGA is mainly involved in plant height and branch growth by regulating the transcription of genes involved in hormone biosynthesis and response. These results indicate that the HAG1-containing SAGA and PAGA complexes are coordinated to regulate gene transcription and development.

2023-01-09 | GSE199760 | GEO

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

2023-01-09 | GSE199757 | GEO

Conserved and plant-specific GCN5-containing complexes cooperate to regulate gene transcription and plant development

Project description:Conserved and plant-specific GCN5-containing complexes cooperate to regulate gene transcription and plant development

| PRJNA821453 | ENA

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

Project description:Conserved and plant-specific GCN5-containing complexes cooperate to regulate gene transcription and plant development [RNA-Seq]

| PRJNA821458 | ENA

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

Project description:Conserved and plant-specific GCN5-containing complexes cooperate to regulate gene transcription and plant development [ChIP-Seq]

| PRJNA821459 | ENA

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

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

| PRJNA899097 | ENA

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

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

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