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Specification and epigenomic resetting of the pig germline exhibit conservation with the human lineage

ABSTRACT: Specification and epigenomic resetting of the pig germline exhibit conservation with the human lineage

PROVIDER: PRJNA648766 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR12327700_1.fastq.gz	Fastqsanger.gz
	SRR12327700_2.fastq.gz	Fastqsanger.gz
	SRR12327800_1.fastq.gz	Fastqsanger.gz
	SRR12327800_2.fastq.gz	Fastqsanger.gz
	SRR12327701_1.fastq.gz	Fastqsanger.gz

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Specification and epigenomic resetting of the pig germline exhibit conservation with the human lineage.

Project description:Investigations of the human germline and programming are challenging because of limited access to embryonic material. However, the pig as a model may provide insights into transcriptional network and epigenetic reprogramming applicable to both species. Here we show that, during the pre- and early migratory stages, pig primordial germ cells (PGCs) initiate large-scale epigenomic reprogramming, including DNA demethylation involving TET-mediated hydroxylation and, potentially, base excision repair (BER). There is also macroH2A1 depletion and increased H3K27me3 as well as X chromosome reactivation (XCR) in females. Concomitantly, there is dampening of glycolytic metabolism genes and re-expression of some pluripotency genes like those in preimplantation embryos. We identified evolutionarily young transposable elements and gene coding regions resistant to DNA demethylation in acutely hypomethylated gonadal PGCs, with potential for transgenerational epigenetic inheritance. Detailed insights into the pig germline will likely contribute significantly to advances in human germline biology, including in vitro gametogenesis.

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Specification and epigenomic resetting of the pig germline exhibit conservation with the human lineage.

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Project description:Recent DepMap CRISPR-Cas9 single gene disruptions have identified genes more essential to proliferation in tissue culture. It would be valuable to translate these finding with measurements more practical for human tissues. Here we show that DepMap essential genes and other literature curated functional genes exhibit cell-specific preferential epigenetic conservation when DNA methylation measurements are compared between replicate cell lines and between intestinal crypts from the same individual. Culture experiments indicate that epigenetic drift accumulates through time with smaller differences in more functional genes. In NCI-60 cell lines, greater targeted gene conservation correlated with greater drug sensitivity. These studies indicate that two measurements separated in time allow normal or neoplastic cells to signal through conservation which human genes are more essential to their survival in vitro or in vivo.

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Project description:Recent attention has focussed on conversion of human pluripotent stem cells to a more naïve transcriptional and epigenetic status. Here we provide a simple method for resetting without transgenes via transient exposure to histone deacetylase inhibition. This protocol is effective across multiple embryo-derived and induced pluripotent stem cells. Reset cells can retain a normal karyotype over multiple passages. Specific markers and global transcriptome profile, including transposable element signature, diverge markedly from conventional human pluripotent stem cells and are consistent with a naïve-like identity. Global DNA methylation is reduced to a level similar to that reported for the inner cell mass, although gain of methylation is also apparent at certain loci. Imprinted methylation is mostly lost, however. In female cells, X chromosome reactivation is evidenced by bi-allelic transcription detected by RNA-FISH. XIST expression is also regained but is predominantly monoallelic. Reset cells are competent for tri-lineage differentiation, both via embryoid body formation and in adherent culture, and can also undergo germline specification. This reliable conversion system and associated transcriptome and methylome datasets will facilitate routine resetting for side by side evaluation with primed pluripotent stem cells and comprehensive interrogation and refinement of candidate naïve pluripotent stem cells.

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