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SUPT3H-less SAGA coactivator can assemble and function without significantly perturbing RNA polymerase II transcription in mammalian cells

ABSTRACT: SUPT3H-less SAGA coactivator can assemble and function without significantly perturbing RNA polymerase II transcription in mammalian cells

PROVIDER: PRJNA734276 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR14701307.fastq.gz	Fastqsanger.gz
	SRR14701308.fastq.gz	Fastqsanger.gz
	SRR14701309.fastq.gz	Fastqsanger.gz
	SRR14701310.fastq.gz	Fastqsanger.gz
	SRR14701311.fastq.gz	Fastqsanger.gz

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SUPT3H-less SAGA coactivator can assemble and function without significantly perturbing RNA polymerase II transcription in mammalian cells

Project description:Co-activator complexes regulate chromatin accessibility and transcription. SAGA (Spt-Ada-Gcn5 Acetyltransferase) is an evolutionary conserved multisubunit co-activator complex with modular organization. The core module of SAGA constitutes the structural heart, composed of a histone octamer like structure and two additional proteins. The central histone octamer like core structure consists of six histone fold domain (HFD)-containing proteins, forming three HF pairs (TADA1/TAF12, TAF6L/TAF9/9b, and TAF10/SUPT7L) in the mammalian SAGA complexes, to which adds SUPT3H, which contains an intramolecular HF pair. The yeast homologue of SUPT3H, called Spt3, was shown to interact genetically and biochemically with the TATA binding protein (TBP). Here we investigated the role of SUPT3H in human U2OS and mouse embryonic stem (ES) cells. Using immuno-purification coupled mass spectrometry experiments we show that both human and mouse SAGA can assemble without the double HFD-containing SUPT3H. Nascent RNA-seq experiments indicted that in either U2OS or mouse ESCs lacking SUPT3H only a small subset of genes is deregulated. Consequently, in mouse ESCs SUPT3H is not essential for mouse ESC survival, but is required for ESC growth and self-renewal. In addition, TBP recruitment experiments show no major change in TBP accumulation at gene promoters in the absence of SUPT3H in mouse and human cells. Taken together our data suggest in mammalian cells SUPT3H is not required for the assembly of SAGA, general TBP recruitment to genes and cell survival, but it is important for regulating a limited set of genes.

2022-07-26 | PXD026991 | Pride

SUPT3H-less SAGA coactivator can assemble and function without significantly perturbing RNA polymerase II transcription in mammalian cells

Project description:To analyse the genome-wide impact of inactivation of the Supt3h subunit of the SAGA complex on RNA polymerase II (Pol II) transcription in human U2OS cells and mouse embryonic stem cells (mESCs), we analysed newly synthesized RNA using 4sU-labelling in mutant and wildtype conditions.

2022-07-06 | GSE175901 | GEO

SUPT3H-less SAGA coactivator can assemble and function without significantly perturbing RNA polymerase II transcription in mammalian cells.

Project description:Coactivator complexes regulate chromatin accessibility and transcription. SAGA (Spt-Ada-Gcn5 Acetyltransferase) is an evolutionary conserved coactivator complex. The core module scaffolds the entire SAGA complex and adopts a histone octamer-like structure, which consists of six histone-fold domain (HFD)-containing proteins forming three histone-fold (HF) pairs, to which the double HFD-containing SUPT3H adds one HF pair. Spt3, the yeast ortholog of SUPT3H, interacts genetically and biochemically with the TATA binding protein (TBP) and contributes to global RNA polymerase II (Pol II) transcription. Here we demonstrate that (i) SAGA purified from human U2OS or mouse embryonic stem cells (mESC) can assemble without SUPT3H, (ii) SUPT3H is not essential for mESC survival, but required for their growth and self-renewal, and (iii) the loss of SUPT3H from mammalian cells affects the transcription of only a specific subset of genes. Accordingly, in the absence of SUPT3H no major change in TBP accumulation at gene promoters was observed. Thus, SUPT3H is not required for the assembly of SAGA, TBP recruitment, or overall Pol II transcription, but plays a role in mESC growth and self-renewal. Our data further suggest that yeast and mammalian SAGA complexes contribute to transcription regulation by distinct mechanisms.

| S-EPMC9371916 | biostudies-literature

The ATAC and SAGA coactivator complexes assemble co-translationally, but their cellular localization properties and functions are distinct

Project description:To understand the precise mechanism that guide the formation of multisubunit complexes is of key importance. Nascent proteins can find and bind their interaction partners during their translation, leading to co-translational assembly. Here we demonstrate that the distinct modules of ATAC (ADA Two A Containing) and SAGA (SPT ADA GCN5 Acetyltransferase), two lysine acetyl transferase-containing transcription coactivator complexes, assemble co-translationally in the cytoplasm of mammalian cells. Fully assembled SAGA complex forms in the cytoplasm of mammalian cells and cytoplasmic SAGA acetylates non-histones proteins, before imported in the nucleus. In contrast, ATAC has no cytoplasmic functions as it cannot be detected in the cytoplasm of mammalian cells. However, fully assembled endogenous ATAC complex containing two functional modules forms and functions in the nucleus. Thus, the two related co-activators, ATAC and SAGA, assemble by using co-translational pathways, but their subcellular localization, cytoplasmic detectability and functions are distinct.

2023-09-27 | PXD038695 | Pride

Project description:SAGA and ATAC are two related transcriptional coactivator complexes, sharing the same histone acetyltransferase (HAT) subunit. The HAT activities of SAGA and ATAC are required for metazoan development but the precise role of the two complexes in RNA polymerase II transcription in mammals is less understood. To determine whether SAGA and ATAC have redundant or specific functions dependent on their HAT activities, we compared the effects of HAT inactivation in each complex with that of inactivation of either SAGA or ATAC core subunits in mouse embryonic stem cells (ESCs). We show that core subunits of SAGA or ATAC subunits are required for complex assembly, mouse ESC growth and self-renewal. Additionally, ATAC, but not SAGA subunits are required for ESC viability by regulating the transcription of translation-related genes. Surprisingly, depletion of specific or shared HAT module subunits caused a global decrease in histone H3K9 acetylation, but did not result in significant phenotypic or transcriptional defects. Thus, our results indicate that SAGA and ATAC are differentially required for viability and self-renewal of mouse ESCs by regulating transcription through different pathways, in a HAT-independent manner.

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.

2011-06-13 | E-MTAB-678 | biostudies-arrayexpress

Two separate roles for the transcription coactivator SAGA and a set of genes redundantly regulated by TFIID and SAGA [RNA]

Project description:Deletions within genes coding for subunits of the transcription coactivator SAGA caused strong genome-wide defects in transcription and SAGA-mediated chromatin modifications. In contrast, rapid SAGA depletion produced only modest transcription defects at 13% of protein-coding genes – genes that are generally more sensitive to rapid TFIID depletion. However, transcription of these “coactivator-redundant” genes is strongly affected by rapid depletion of both factors, showing the overlapping functions of TFIID and SAGA at this gene set. We suggest that this overlapping function is linked to TBP-DNA recruitment. The remaining 87% of expressed genes that we term “TFIID-dependent” are highly sensitive to rapid TFIID depletion and insensitive to rapid SAGA depletion. Genome-wide mapping of SAGA and TFIID found binding of both factors at many genes independent of gene class. DNA analysis suggests that the distinction between the gene classes is due to multiple components rather than any single regulatory factor or promoter sequence motif.

2020-01-09 | GSE133004 | GEO

Two separate roles for the transcription coactivator SAGA and a set of genes redundantly regulated by TFIID and SAGA [ChIP-Seq]

2020-01-09 | GSE142183 | GEO

Two separate roles for the transcription coactivator SAGA and a set of genes redundantly regulated by TFIID and SAGA [RNA-Seq]

2020-01-09 | GSE142182 | GEO

Two separate roles for the transcription coactivator SAGA and a set of genes redundantly regulated by TFIID and SAGA [ChEC-Seq]

2020-01-09 | GSE142120 | GEO