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Spatio-temporal X-linked gene reactivation in the mouse germline reveals site-specific retention of epigenetic silencing [WGBS]

ABSTRACT: Spatio-temporal X-linked gene reactivation in the mouse germline reveals site-specific retention of epigenetic silencing [WGBS]

PROVIDER: PRJNA1020774 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR26161215.fastq.gz	Fastqsanger.gz
	SRR26161216.fastq.gz	Fastqsanger.gz

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Spatio-temporal X-linked gene reactivation in the mouse germline reveals site-specific retention of epigenetic silencing [WGBS]

Project description:Random X-chromosome inactivation (XCI) is a hallmark of female mammalian somatic cells. This epigenetic mechanism, mediated by the long non-coding RNA Xist, occurs in the epiblast and is stably maintained to ensure proper dosage compensation of X-linked genes during life. However, this silencing is lost during primordial germ cell (PGC) development. Using a combination of single-cell allele-specific RNA sequencing and low-input chromatin profiling on in vivo developing mouse PGC, we provide unprecedented detailed maps of gene reactivation. We demonstrate that PGC still carry a fully silent X chromosome at embryonic day (E) 9.5, despite the loss of Xist expression. X-linked genes are then gradually reactivated outside the Xist first-bound regions. At E12.5, a significant part of the inactive X chromosome (Xi) still resists reactivation, carrying an epigenetic memory of its silencing. Late-reactivated genes are enriched in repressive chromatin marks, including DNA methylation and H3K27me3 marks. Our results define the timing of reactivation of the silent X chromosome a key event in female PGC reprogramming with direct implications for reproduction.

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Spatio-temporal X-linked gene reactivation in the mouse germline reveals site-specific retention of epigenetic silencing

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Spatio-temporal X-linked gene reactivation in the mouse germline reveals site-specific retention of epigenetic silencing [RNA-seq]

Project description:Spatio-temporal X-linked gene reactivation in the mouse germline reveals site-specific retention of epigenetic silencing [RNA-seq]

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Retention of paternal epigenetic memory in the developing teleost germline [WGBS]

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Spatio-temporal X-linked gene reactivation in the mouse germline reveals site-specific retention of epigenetic silencing

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

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Retention of paternal epigenetic memory in the developing teleost germline [WGBS]

Project description:Two waves of DNA methylation reprogramming occur during mammalian embryogenesis; during preimplantation development and during primordial germ cell (PGC) formation. However, it is currently unclear how evolutionarily conserved these processes are. Here we characterize the DNA methylomes of zebrafish PGCs at four developmental stages and unravel retention of paternal epigenetic memory, in stark contrast with the findings in mammals. Gene expression profiling of zebrafish PGCs at same developmental stages revealed that the embryonic germline is defined by a small number of markers that display strong developmental stage-specificity and that are uncoupled from DNA methylation-mediated regulation.

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Reactivation of the silenced X-chromosome during mouse germline development

Project description:X chromosome reactivation (XCR) occurs over a prolonged period during genome-wide reprogramming in female germ cells, initiating soon after primordial germ cell specification. The kinetics of XCRs remain poorly understood, as previous studies of XCR were based on a few genes. For a global appraisal of XCR dynamics, we performed single-cell RNA-seq on F1 female (XX(Xist∆)) and male (XY) germ cells from E9.5 to E16.5 stages in development. Through the incorporation of interspecific crosses between C57B6J (B6) and Castaneus (CAST) parental mouse strains, containing a high number of informative single-nucleotide variants, we are able to distinguish gene expression from parental chromosomes in F1 embryos computationally.

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Protemics of human cell during HHV-6A reactivation

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