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Systematic Identification of Factors Crucial for Provirus Silencing in Embryonic Stem Cells

ABSTRACT: Systematic Identification of Factors Crucial for Provirus Silencing in Embryonic Stem Cells

PROVIDER: PRJNA289720 | ENA |

REPOSITORIES: ENA

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Systematic Identification of Factors Crucial for Provirus Silencing in Embryonic Stem Cells (RNA-seq)

Project description:Our study reports the first genome-wide atlas of functional nodes that mediate proviral silencing in ESCs. It provides evidences for the comprehensive, interconnected and multi-layered genetic/epigenetic machineries by which ESCs maintain the repressive state of provirus and ERVs. RNA-seq analysis to determine the regulated endogenous retroviruses by Histone chaperones (Chaf1a/b), sumoylation factors (Sumo2/ Ube2i/Sae1/Uba2/Senp6) and chromatin modifiers (Trim28/Eset/Atf7ip)

2015-09-14 | E-GEOD-70863 | biostudies-arrayexpress

Systematic Identification of Factors Crucial for Provirus Silencing in Embryonic Stem Cells (ChIP-seq)

Project description:Our study reports the first genome-wide atlas of functional nodes that mediate proviral silencing in ESCs. It provides evidences for the comprehensive, interconnected and multi-layered genetic/epigenetic machineries by which ESCs maintain the repressive state of provirus and ERVs. ChIP-seq analysis of Chaf1a, Trim28, Sumo2 and Zfp809 to demonstrate the mechanism of the silencing of Endogenous retroviruses

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Systematic Identification of Factors Crucial for Provirus Silencing in Embryonic Stem Cells (RNA-seq)

2015-09-14 | GSE70863 | GEO

Systematic Identification of Factors Crucial for Provirus Silencing in Embryonic Stem Cells (ChIP-seq)

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Project description:Systematic Identification of Factors Crucial for Provirus Silencing in Embryonic Stem Cells (ChIP-seq)

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Mus musculus

Project description:Systematic Identification of Factors Crucial for Provirus Silencing in Embryonic Stem Cells (RNA-seq)

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Systematic Identification of Factors Crucial for Provirus Silencing in Embryonic Stem Cells

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2015-09-14 | E-GEOD-70865 | biostudies-arrayexpress

Systematic Identification of Factors Crucial for Provirus Silencing in Embryonic Stem Cells

Project description:This SuperSeries is composed of the SubSeries listed below.

2015-09-14 | GSE70865 | GEO

Systematic identification of factors involved in the silencing of germline genes in mouse embryonic stem cells

Project description:In mammals, many germline genes are repressed by epigenetic mechanisms to prevent their illegitimate expression in embryonic and somatic cells. To advance our understanding of the complete mechanisms restricting the expression of germline genes in mammals, we analyzed the chromatin signature of germline genes and performed a genome-wide CRISPR-Cas9 knock-out screen for genes involved in germline gene repression using a reporter system in which GFP is under the control of the epigenetically repressed Dazl germline promoter in mouse embryonic stem cells (ESCs). We showed that the repression of germline genes mainly depends on the polycomb complex PRC1.6 and DNA methylation, which function additively in mouse ESCs. Furthermore, we identified and validated several novel genes involved in the repression of germline genes, and characterized three of them: Usp7, Shfm1 (also known as Sem1) and Erh. Inactivation of Usp7, Shfm1 or Erh led to the upregulation of germline genes, as well as retrotransposons for Shfm1, in mouse ESCs. Functionally, Usp7 acts at two levels: firstly it associates with PRC1.6 components and represses germline genes independently of DNA methylation, and secondly it facilitates DNA methylation deposition at germline genes for long term repression. In summary, our study provides a global view of the epigenetic mechanisms and novel factors required for silencing germline genes in embryonic cells.

2023-02-03 | PXD030666 | Pride

Systematic Analysis of Allelic Silencing Defines the Interplay of Key Pathways in Xist-mediated Chromosome Inactivation

Project description:Xist RNA, the master regulator of X chromosome inactivation, acts in cis to induce chromosome silencing through the stepwise recruitment of factors that modify underlying chromatin structure. Whilst considerable progress has been made towards defining key silencing factors and the elements to which they bind, their relative contribution to silencing different genes, and their relationship with one another is poorly understood. Here we describe a systematic analysis of Xist-mediated allelic silencing in ES cell-based models. We show that Spen, recruited through the Xist A-repeat, plays a central role, being critical for silencing of all except a subset of low expressed genes. Polycomb, recruited through the Xist B/C-repeat, also plays a key role, favouring silencing of genes with pre-existing H3K27me3 chromatin. LBR and the Rbm15-Mettl3/14 m6A-methyltransferase complex, previously proposed to have a central role, make at most a minor contribution to gene silencing. We integrate our findings in a comprehensive model for Xist-mediated chromosome silencing.

2019-06-17 | GSE119602 | GEO

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