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

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

PROVIDER: PRJNA821459 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR18534267_1.fastq.gz	Fastqsanger.gz
	SRR18534267_2.fastq.gz	Fastqsanger.gz
	SRR18534268_1.fastq.gz	Fastqsanger.gz
	SRR18534268_2.fastq.gz	Fastqsanger.gz
	SRR18534269_1.fastq.gz	Fastqsanger.gz

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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 [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.

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

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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 [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

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

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

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

Project description:This SuperSeries is composed of the SubSeries listed below.

2023-01-09 | GSE199761 | GEO

Project description:The telomere repeat binding factors TRB1, TRB2, and TRB3 (TRB1/2/3) in Arabidopsis thaliana not only function as components of the PEAT complex involved in histone acetylation and H2A deubiquitination but also interact with Polycomb Repressive Complex 2 (PRC2) involved in H3 lysine 27 trimethylation (H3K27me3). In this study, we demonstrate that TRB1/2/3 form two additional chromatin-associated complexes, which we term TRB1/2/3-HTH1/2/3 (TRHT) and TRB1/2/3-HISTONE-DEMETHYLASE (TRHD). The TRHT complex comprises TRB1/2/3, ICU11, and HTH1/2/3, whereas the TRHD complex is composed of TRB1/2/3, ICU11, ZDP2, JMJ14, and NAC050/052. The TRHT and TRHD (TRHT/TRHD) complexes occupy a common set of target genes and cooperate to mediate JMJ14-mediated H3K4me3 demethylation and transcriptional repression. Compared with PEAT and PRC2 target genes, which are characterized by high and low levels of H3K4me3, respectively, the TRHT/TRHD target genes exhibit low to medium levels of H3K4me3. At the whole-genome level, TRB1/2/3 repress transcription at TRHT/TRHD and PRC2 target genes, while facilitating transcription at PEAT target genes. At the TRHT/TRHD target genes, the TRHT/TRHD complexes mediate transcriptional repression through both H3K4me3 demethylation-dependent and –independent mechanisms. These findings reveal the molecular mechanisms by which how the TRHT/TRHD complexes are coordinated with the PEAT and PRC2 complex to ensure the orchestration of multiple histone modifications at the whole-genome level.

2025-09-17 | GSE287720 | GEO

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