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Germ cell specific high level of H3K9me3 in chicken PGCs: distribution and role in gene expression control [ChIP-Seq]

ABSTRACT: Germ cell specific high level of H3K9me3 in chicken PGCs: distribution and role in gene expression control [ChIP-Seq]

PROVIDER: PRJNA1046235 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR26965729_1.fastq.gz	Fastqsanger.gz
	SRR26965729_2.fastq.gz	Fastqsanger.gz
	SRR26965730_1.fastq.gz	Fastqsanger.gz
	SRR26965730_2.fastq.gz	Fastqsanger.gz
	SRR26965731_1.fastq.gz	Fastqsanger.gz

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Germ cell specific high level of H3K9me3 in chicken PGCs: distribution and role in gene expression control [RNA-Seq]

Project description:Chicken primordial germ cells (PGCs) have an epigenetic signature which differs from the one that mammalian PGCs acquire with their epigenome reprogramming during early embryonic development. In particular, chicken PGCs display a high global amount of histone H3 lysine 9 trimethylation (H3K9me3) compared to somatic cell types. We performed the genome-wide profiling of H3K9me3 and the transcriptome analysis on chicken PGCs compared to embryonic stem cells (ESCs) as a closely related, non germinal cell type.

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Germ cell specific high level of H3K9me3 in chicken PGCs: distribution and role in gene expression control [ChIP-Seq]

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Germ cell specific high level of H3K9me3 in chicken PGCs: distribution and role in gene expression control

Project description:Germ cell specific high level of H3K9me3 in chicken PGCs: distribution and role in gene expression control

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Germ cell specific high level of H3K9me3 in chicken PGCs: distribution and role in gene expression control [RNA-Seq]

Project description:Germ cell specific high level of H3K9me3 in chicken PGCs: distribution and role in gene expression control [RNA-Seq]

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Expression data from cultured chicken primordial germ cells (PGCs)

Project description:The growth factors and signaling pathways that are essential for the inducing proliferation of chicken PGCs is unclear. We investigated the effect of basic fibroblast growth factor (bFGF) on the survival and proliferation of PGCs under feeder-free conditions. We used microarrays to examine the genes regulated by bFGF treatment in chicken PGCs. Cultured PGCs were collected before and after withdrawal of bFGF for 24 h, and 24 h after bFGF replacement. The RNA was extracted and hybridized on Affymetrix microarrays. Three replicates each.

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Expression data from cultured chicken primordial germ cells (PGCs)

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Project description:In poultry, in vitro derived primordial germ cells (PGCs) represent an important tool for management of genetic resources. However, several studies have highlighted sexual differences exhibited by PGCs through in vitro steps, which may compromise their reproductive capacities. To understand this phenomenon, we compared the proteome of pregonadal chicken male (ZZ) and female (ZW) PGCs expanded in vitro by quantitative proteomic analysis using a GeLC-MS/MS strategy. The proteins found to be differentially abundant in chicken male and female PGCs indicated their early sexual identity. Many of the proteins up-accumulated in male PGCs were encoded by genes strongly enriched in the sexual chromosome Z. This suggests that the known lack of dosage compensation of the transcription of Z-linked genes between sexes persists at protein level in PGCs, and that this may be a key factor of their autonomous sex differentiation. Male and female PGCs up-accumulated protein sets were associated with differential biological processes, and contained proteins biologically relevant for male and female germ cell development respectively. This study presents first evidence on early predetermined sex specific cell fate of chicken PGCs that will help to understand their sexual physiological specificities and enable more precise sex-specific adaptation of in vitro culture conditions.

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Germ cell specific high level of H3K9me3 in chicken PGCs: distribution and role in gene expression control

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

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Setdb1 is required for persistence of H3K9me3 and repression of endogenous retroviruses in mouse primordial germ cells

Project description:Transcription of endogenous retroviruses (ERVs) is inhibited by de novo DNA methylation during gametogenesis, a process initiated after birth in oocytes and at ~E15.5 in prospermatogonia. Earlier in germline development however, the genome, including most retrotransposons, is progressively demethylated, with young ERVK and ERV1 elements retaining intermediate methylation levels. As DNA methylation reaches a low point in E13.5 primordial germ cells (PGCs) of both sexes, we determined whether retrotransposons are marked by H3K9me3 and H3K27me3 using a recently developed low input ChIP-seq method. Although these repressive histone modifications are predominantly found on distinct genomic regions in E13.5 PGCs, they concurrently mark partially methylated LTRs and LINE1 elements. Germline-specific conditional knock-out (KO) of the H3K9 methyltransferase SETDB1 yields a decrease of both histone marks and DNA methylation at H3K9me3 enriched retrotransposon families. Strikingly, Setdb1-KO E13.5 PGCs show concomitant de-repression of many marked ERVs, including IAP, ETn and ERVK10C elements and ERV-proximal genes, a subset in a sex-dependent manner. Furthermore, Setdb1 deficiency is associated with a reduced number of male PGCs and postnatal hypogonadism in both sexes. Taken together, these observations reveal that SETDB1 is an essential guardian against proviral expression prior to the onset of de novo DNA methylation in the germline. H3K9me3, H3K27me3 and expression profiles in Setdb1 WT, Het and KO male and female E13.5 PGCs.

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