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Genome stability in different mouse embryonic stem cells [ATAC-seq]

ABSTRACT: Genome stability in different mouse embryonic stem cells [ATAC-seq]

PROVIDER: PRJNA663161 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR12630463_1.fastq.gz	Fastqsanger.gz
	SRR12630463_2.fastq.gz	Fastqsanger.gz
	SRR12630464_1.fastq.gz	Fastqsanger.gz
	SRR12630464_2.fastq.gz	Fastqsanger.gz
	SRR12630465_1.fastq.gz	Fastqsanger.gz

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Genome stability in different mouse embryonic stem cells

Project description:Genome stability in different mouse embryonic stem cells

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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

Genome stability in different mouse embryonic stem cells [exome-seq]

Project description:Genome stability in different mouse embryonic stem cells [exome-seq]

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Genome stability in different mouse embryonic stem cells [ATAC-seq]

Project description:Naïve mouse ESCs exhibit full term developmental competence thus hold great potential in regenerative medicine. Maintaining genome stability is essential for potential application of ESCs in stem cell therapy. While ESC potency fluctuate with retrovirus activity, it is unclear whether long-term cultures affect retrotransposition and genomic stability. We compared retrotransposons in naïve ESCs using various approaches. We show that feeder-serum based culture conditions and small molecule LCDM maintain appropriate expression of retrovirus activity following long-term cultures, whereas cultures under 2iLif and a2i result in aberrant upregulation of retrotransposons. This leads to high frequent retrotransposition. Moreover, naïve ESCs on feeder-serum based culture conditions and small molecule LCDM still generate complete ESC pups by TEC assay, functional test of pluripotency, following long-term cultures, despite that all culture conditions maintain high expression levels of pluripotent genes such as Oct4, Nanog, Klf4 and Sox2. Meanwhile, long telomeres are maintained in ESCs under cultures in Feeder-serum and LCDM conditions but telomeres shortened in other conditions with increasing passages. These data provide insights into retrotransposition, genomic stability and pluripotency of naïve ESCs.

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Genome stability in different mouse embryonic stem cells

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ATAC-seq of mouse embryonic stem cells

Project description:To identify the accessible chromatin in wild-type mouse embryonic stem cells (mESCs), we performed ATAC-seq in mESCs.

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Genome stability in different mouse embryonic stem cells [exome-seq]

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Biological Insights from the genome Sequences of Human Embryonic Stem Cell Lines

Project description:<p>Human embryonic stem cells (hESCs) are a powerful tool for the study of human development and can form the basis of cellular disease models or therapies. However, the genetic make-up and stability of hESCs has not been systematically studied at a genome-wide level with single nucleotide resolution. We therefore sequenced the whole exomes of widely available hESCs. The data generated has provided new insights about the nature of acquired variation and the genomic integrity of the cell lines. We anticipate that this online resource will enable investigators to access raw sequencing data in order to interrogate cell lines for different disease and trait-associated genetic variants.</p>

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ATAC-seq of mouse embryonic stem cells

Project description:ATAC-seq of mouse embryonic stem cells

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