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Nucleome programming is required for the foundation of totipotency in mammalian germline development [NET-CAGE]

ABSTRACT: Nucleome programming is required for the foundation of totipotency in mammalian germline development [NET-CAGE]

PROVIDER: PRJNA762043 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR15831523.fastq.gz	Fastqsanger.gz
	SRR15831524.fastq.gz	Fastqsanger.gz
	SRR15831525.fastq.gz	Fastqsanger.gz
	SRR15831526.fastq.gz	Fastqsanger.gz
	SRR15831527.fastq.gz	Fastqsanger.gz

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Nucleome programming is required for the foundation of totipotency in mammalian germline development [NET-CAGE]

Project description:Germ cells are unique in engendering totipotency, yet the mechanisms underlying this capacity remain elusive. Here, we perform comprehensive and in-depth nucleome analysis of mouse germ-cell development in vitro, encompassing pluripotent precursors, primordial germ cells (PGCs) before and after epigenetic reprogramming, and spermatogonia/spermatogonial stem cells (SSCs). Although epigenetic reprogramming, including genome-wide DNA de-methylation, creates broadly open chromatin with abundant enhancer-like signatures, the augmented chromatin insulation safeguards transcriptional fidelity. These insulatory constraints are then erased en masse for spermatogonial development. Notably, despite distinguishing epigenetic programming, including global DNA re-methylation, the PGCs-to-spermatogonia/SSCs development entails further euchromatization. This accompanies substantial erasure of lamina-associated domains, generating spermatogonia/SSCs with a minimal peripheral attachment of chromatin except for pericentromeres—an architecture conserved in primates. Accordingly, faulty nucleome maturation, including persistent insulation and improper euchromatization, leads to impaired spermatogenic potential. Given that PGCs after epigenetic reprogramming serve as oogenic progenitors as well, our findings elucidate a principle for the nucleome programming that creates gametogenic progenitors in both sexes, defining a basis for nuclear totipotency.

2022-06-15 | GSE183807 | GEO

Nucleome programming is required for the foundation of totipotency in mammalian germline development [ChIP-Seq]

2022-06-15 | GSE183826 | GEO

Nucleome programming is required for the foundation of totipotency in mammalian germline development [Hi-C]

2022-06-15 | GSE184129 | GEO

Nucleome programming is required for the foundation of totipotency in mammalian germline development [ATAC-Seq]

2022-06-15 | GSE183801 | GEO

Nucleome programming is required for the foundation of totipotency in mammalian germline development

Project description:Nucleome programming is required for the foundation of totipotency in mammalian germline development

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Nucleome programming is required for the foundation of totipotency in mammalian germline development [Hi-C]

Project description:Nucleome programming is required for the foundation of totipotency in mammalian germline development [Hi-C]

| PRJNA763350 | ENA

Nucleome programming is required for the foundation of totipotency in mammalian germline development [ChIP-Seq]

Project description:Nucleome programming is required for the foundation of totipotency in mammalian germline development [ChIP-Seq]

| PRJNA762069 | ENA

Nucleome programming is required for the foundation of totipotency in mammalian germline development [ATAC-Seq]

Project description:Nucleome programming is required for the foundation of totipotency in mammalian germline development [ATAC-Seq]

| PRJNA762033 | ENA

NET-CAGE Characterizes the Dynamics and Topology of Human Transcribed Cis-regulatory Elements

Project description:Promoters and enhancers are key cis-regulatory elements, but how they operate to generate cell-type-specific transcriptomes is not fully understood. We developed a simple and robust approach to sensitively detect 5’-ends of nascent RNAs (NET-CAGE) in diverse cells and tissues, including unstable transcripts such as enhancer-derived RNAs. We studied RNA synthesis and degradation at the transcription start site (TSS) level, characterizing the impact of differential promoter usage on transcript stability. We quantified transcription from cis-regulatory elements without the influence of RNA turnover, and show that enhancer-promoter pairs are generally activated simultaneously upon stimulation. By integrating NET-CAGE data with chromatin interaction maps, we show that cis-regulatory elements are topologically connected according to their cell-type specificity. We identified new enhancers with high sensitivity, and delineated primary locations of transcription within super-enhancers. Our NET-CAGE dataset derived from human and mouse cells expands the FANTOM5 catalogue of transcribed enhancers, with broad applicability to biomedical research.

2019-06-10 | GSE118075 | GEO

Nucleome programming is required for the foundation of totipotency in mammalian germline development.

Project description:Germ cells are unique in engendering totipotency, yet the mechanisms underlying this capacity remain elusive. Here, we perform comprehensive and in-depth nucleome analysis of mouse germ-cell development in vitro, encompassing pluripotent precursors, primordial germ cells (PGCs) before and after epigenetic reprogramming, and spermatogonia/spermatogonial stem cells (SSCs). Although epigenetic reprogramming, including genome-wide DNA de-methylation, creates broadly open chromatin with abundant enhancer-like signatures, the augmented chromatin insulation safeguards transcriptional fidelity. These insulatory constraints are then erased en masse for spermatogonial development. Notably, despite distinguishing epigenetic programming, including global DNA re-methylation, the PGCs-to-spermatogonia/SSCs development entails further euchromatization. This accompanies substantial erasure of lamina-associated domains, generating spermatogonia/SSCs with a minimal peripheral attachment of chromatin except for pericentromeres-an architecture conserved in primates. Accordingly, faulty nucleome maturation, including persistent insulation and improper euchromatization, leads to impaired spermatogenic potential. Given that PGCs after epigenetic reprogramming serve as oogenic progenitors as well, our findings elucidate a principle for the nucleome programming that creates gametogenic progenitors in both sexes, defining a basis for nuclear totipotency.

| S-EPMC9251848 | biostudies-literature

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