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

ABSTRACT: 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.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE217485 | 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]

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2023-01-09 | GSE199760 | GEO

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: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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Project description:The SAGA (Spt-Ada-Gcn5 acetyltransferase) complex is an evolutionarily conserved, multifunctional co-activator complex, which has a critical role in histone acetylation, gene expression, and various developmental processes in eukaryotes. However, little is known about the composition and function of the SAGA complex in plants. Here, we found that the SAGA complex in Arabidopsis thaliana contains not only conserved subunits and but also four plant-specific subunits, including three homologous subunits, SCS1, SCS2A, and SCS2B (SCS1/2A/2B), and a TAF-like subunit, TAFL. We also found that a series of SAGA subunits are shared in yeast and/or metazoans but are absent in Arabidopsis. Mutations in the unique SAGA subunits SCS1/2A/2B lead to defective phenotypes similar to those caused by mutations in the conserved SAGA subunits HAG1 and ADA2B; these defective phenotypes include delayed juvenile-to-adult phase transition, late flowering, and increased trichome density. SCS1/2A/2B function in the SAGA complex to promote the transcription of development-related genes by facilitating histone H3 acetylation. The results suggest that, compared to SAGA complexes in other eukaryotes, the SAGA complex in plants has evolved unique features that are necessary for normal growth and development.

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2021-08-11 | PXD027026 | Pride

Tra1 has specific regulatory roles, rather than global functions, within the SAGA coactivator complex

Project description:The SAGA complex is a conserved, multifunctional coactivator that plays broad roles in eukaryotic transcription. Previous studies suggested that Tra1, the largest SAGA component, is required either for SAGA assembly or for recruitment by DNA-bound transcriptional activators. In contrast to S. cerevisiae and mouse, a tra1? mutant is viable in S. pombe, allowing us to test these issues in vivo. We find that, in a tra1? mutant, SAGA assembles and is recruited to some, but not all promoters. Consistent with these findings, Tra1 regulates the expression of only a subset of SAGA-dependent genes. We previously reported that the SAGA subunits Gcn5 and Spt8 have opposing regulatory roles during S. pombe sexual differentiation. We show here that, like Gcn5, Tra1 represses this pathway, although by a distinct mechanism. Thus, our study reveals that Tra1 has specific regulatory roles, rather than global functions, within SAGA.

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Project description:In Saccharomyces cerevisiae, the SAGA complex regulates its own activity by undergoing multimerization. This multimerization is triggered by SAGA autoacetylation at three sites on its Ada3 subunit, allowing recognition of this acetylation by the bromodomain of the Gcn5/Spt7 SAGA subunit. Once multimerized, SAGA is capable of cooperatively acetylating chromatin, and an inability to autoacetylate Ada3 leads to transcriptional and phenotypic defects in a wide range of stress-activated genes. The SAGA multimerization increased significantly in media with Sucorse as the only carbon resource than that with Glucose. In this study, the high-throughput sequence of wild type (WT) strain, Ada3 acetylation mutant (Ada3-3KR), Gcn5 bromodomain mutant (Gcn5m) and Spt7 bromodomain mutant (Spt7m) indicate a new function for Ada3 acetylation, show which genes transcription can be regulated by SAGA multimers.

2021-11-29 | GSE161887 | GEO

The SAGA complex in the rice pathogen Fusarium fujikuroi: structure and functional characterization

Project description:Post-translational modification of histones is a crucial mode of transcriptional regulation in eukaryotes. A well-described acetylation modifier of certain lysine residues is the Spt-Ada-Gcn5 acetyltransferase (SAGA) complex assembled around the histone acetyltransferase Gcn5 in Saccharomyces cerevisiae. We identified and characterized the SAGA complex in the rice pathogen Fusarium fujikuroi, well-known for producing a large variety of secondary metabolites (SMs). By using a co-immunoprecipitation approach, almost all of the S. cerevisiae SAGA complex components have been identified, except for the ubiquitinating DUBm module and the chromodomain containing Chd1. Deletion of GCN5 led to impaired growth, loss of conidiation and alteration of SM biosynthesis. Furthermore, we show that in F. fujikuroi Gcn5 is essential for the acetylation of several histone 3 lysines, i.e. H3K4, H3K9, H3K18 and H3K27. A genome-wide microarray analysis revealed differential expression of about 30% of the genome with an enrichment of genes involved in primary and secondary metabolism, transport and histone modification. HPLC-based analysis of known SMs revealed significant alterations in the Δgcn5 mutant. While most SM genes were activated by Gcn5 activity, the biosynthesis of the pigment bikaverin was strongly increased upon GCN5 deletion underlining the diverse roles of the SAGA complex in F. fujikuroi. Investigation of whole genome gene expression of the Fusarium fujikuroi wild type IMI58289 and the Δgcn5 mutant under nitrogen starvation and nitrogen sufficient conditions.

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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.

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