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Mus musculus

ABSTRACT: Expression and ChIP-seq analyses of embryonic stem cells, extraembryonic endoderm stem cells, and trophoblast stem cells

PROVIDER: PRJNA115689 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR038973.fastq.gz	Fastqsanger.gz
	SRR038974.fastq.gz	Fastqsanger.gz
	SRR038975.fastq.gz	Fastqsanger.gz
	SRR038976.fastq.gz	Fastqsanger.gz
	SRR038977.fastq.gz	Fastqsanger.gz

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Expression and ChIP-seq analyses of embryonic stem cells, extraembryonic endoderm stem cells, and trophoblast stem cells

Project description:Bivalent histone domains have been proposed to contribute to pluripotency in embryonic stem cells, suggesting an epigenetic mechanism may regulate stem cell behavior in general. Here we compare histone modifications in two other stem cells derived from the blastocyst. We show that extraembryonic stem cells have little repressive lysine 27 trimethylation and few bivalent domains. Thus, bivalent domains are not a common mechanism for maintaining the undifferentiated state in blastocyst-derived stem cells and alternative mechanisms must mediate transcriptional repression in extraembryonic cells. We show that lysine 9 trimethylation, but not DNA methylation, is likely to fulfill this role. Intriguingly, although we do detect bivalent domains in pluripotent cells in the early mouse embryo, the epigenetic status of extraembryonic cells does not entirely reflect their in vitro stem cell counterparts. Therefore, differences in epigenetic regulation between lineage progenitors in vivo and in vitro may arise during selection for self-renewal in vitro. Expression profiles [GSM388878-GSM388881] of three different stem cells (R1 embryonic stem cells, trophoblast stem cells, extraembryonic endoderm stem cells) were generated for comparison to CHIP-seq data [GSM392044-GSM392055] of the same three stem cell lines to observe correlations with Histone 3 K4 and K27 trimethylation patterns. CHIP-seq details: R1 embryonic stem cells, trophoblast stem cells or extraembryonic endoderm stem cells were grown, lysed and chromatin purified. The chromatin was immunoprecipitated for either histone 3 K4 trimethylation or histone 3 K27 trimethylation and the immunoprecipitate was subjected to purification and high-throughput Illumina-based sequencing.

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Project description:Genome-Wide Sox17 Binding Sites in Mouse Extraembryonic Endoderm and Embryonic Stem Cells

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Dissecting crosstalk between embryonic and extra-embryonic tissues with stem cell co-culture [I]

Project description:Faithful embryogenesis requires the precise coordination between embryonic and extraembryonic tissues. Although embryonic and extraembryonic stem cells have been derived from several mammalian species including humans, they are cultured in different conditions, which makes it difficult to study their intercommunication. Here, by simultaneously activating FGF, TGF-β and WNT pathways, we derived stable pluripotent stem cells (PSCs), trophoblast stem cells (TSCs) and extraembryonic endoderm stem cells (XENs) from mouse blastocysts under the same condition (FTW). Co-culture of PSCs and XENs in the same environment uncovered, among other interactions, a previously unrecognized control of proliferation of epiblast cells by extraembryonic endoderm cells. FTW condition also supported de novo derivation of XENs from cynomolgus monkey and human blastocysts, and enabled setting up co-culture of human iPSCs and XENs. Crosspieces comparison revealed conserved and divergent processes and genes regulating XENs and ligand-receptor interactions between pluripotent and extraembryonic endoderm cells. Our study establishes a unique stem cell co-culture strategy to examine embryonic and extraembryonic lineage crosstalk during early mammalian development, and opens the door for developing more faithful in vitro models and differentiation protocols.

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Transcriptomics of trophoblast stem cells and extraembryonic endoderm stem cells

Project description:To identify splicing regulators with unique regulation in placenta and the trophectoderm lineage, we sequenced trophoblast stem (TS) and Extraembryonic endoderm stem (XEN) cells.

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