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Newly synthesized RNA analysis in WT, SAGA and ATAC mutant mouse embryonic stem cells

ABSTRACT: Newly synthesized RNA analysis in WT, SAGA and ATAC mutant mouse embryonic stem cells

PROVIDER: PRJNA734282 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR14701240.fastq.gz	Fastqsanger.gz
	SRR14701241.fastq.gz	Fastqsanger.gz
	SRR14701242.fastq.gz	Fastqsanger.gz
	SRR14701243.fastq.gz	Fastqsanger.gz
	SRR14701244.fastq.gz	Fastqsanger.gz

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Newly synthesized RNA analysis in WT, SAGA and ATAC mutant mouse embryonic stem cells

Project description:To analyse the genome-wide impact of inactivation of the ATAC or SAGA coactivator complexes on RNA polymerase II (Pol II) transcription, we purified newly synthesized RNA from mutant mouse embryonic stem (ES) cell lines in which subunits of ATAC (Yeats2, Zzz3) or SAGA (Supt7l) are inactivated or depleted. We also performed this analysis in mutant cell lines in which a subunit (Tada3) of the shared histone acetyltransferase activity of these two complexes is depleted. Newly synthesized RNA was purified following the 4sU labelling method (more details in extract protocol). For two wildtype samples, the total RNA input was also analysed.

2021-08-03 | GSE175904 | GEO

ATAC-seq in WT, SAGA and ATAC mutant mouse embryonic stem cells

Project description:Assess chromatin accessibility in WT and mutant ES E14 strains using ATAC-seq. Mutant strains are depleted for subunits of the coactivator complexes SAGA (Supt7l KO) or ATAC (Yeats2, Zzz3) using constitutive knock-out (KO) or the auxin-inducible degron (AID) system.

2021-08-03 | GSE175902 | GEO

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.

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H3K9ac ChIP-seq in WT, SAGA and ATAC mutant mouse embryonic stem cells

Project description:Assess H3K9ac levels in WT and mutant ES E14 strains using ChIP-seq. Mutant strains are depleted for subunits of the coactivator complexes SAGA (Supt7l KO) or ATAC (AID-Yeats2) or of HAT subunits (AID-Tada3, Tada2a+Tada2b KO) using constitutive knock-out (KO) or the auxin-inducible degron (AID) system.

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ATAC-seq in WT, SAGA and ATAC mutant mouse embryonic stem cells

Project description:ATAC-seq in WT, SAGA and ATAC mutant mouse embryonic stem cells

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SAGA Is a General Cofactor for RNA Polymerase II Transcription

Project description:The SAGA co-activator has been implicated in the regulation of a smal subset of genes in budding yeast in transcriptomic analyses performed in steady-state levels of RNA. We used microarrays to analyse newly-synthesized RNA in several mutants for the SAGA complex to disclose and readdress the impact of this complex in RNA Polymerase II transcription.

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

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