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

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE199761 | GEO | 2023/01/09

REPOSITORIES: GEO

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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.

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

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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

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

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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]

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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]

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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 intergenic elements and DNA methylation cooperate to regulate transcription at the il17 locus.

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