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In vitro capture and characterization of embryonic rosette-stage pluripotency between naive and primed states (I, bulk RNA-Seq data)

ABSTRACT: In vitro capture and characterization of embryonic rosette-stage pluripotency between naive and primed states (I, bulk RNA-Seq data)

PROVIDER: PRJNA415252 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR6200670.fastq.gz	Fastqsanger.gz
	SRR6200671.fastq.gz	Fastqsanger.gz
	SRR6200681.fastq.gz	Fastqsanger.gz
	SRR6200672.fastq.gz	Fastqsanger.gz
	SRR6200682.fastq.gz	Fastqsanger.gz

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In vitro capture and characterization of embryonic rosette-stage pluripotency between naive and primed states

Project description:Upon implantation, the naive pluripotent epiblast of the mouse blastocyst generates a rosette, undergoes lumenogenesis and forms the primed pluripotent egg cylinder, able to generate the embryonic tissues. How pluripotency progression and morphogenesis are linked, and whether intermediate pluripotent states exist remain controversial. We identify here a rosette pluripotent state, defined by co-expression of naive factors with transcription factor OTX2. Downregulation of blastocyst WNT signals drives transition into rosette pluripotency by inducing OTX2. The rosette then activates MEK signals that induce lumenogenesis and drive progression to primed pluripotency. Consequently, combined WNT and MEK inhibition supports rosette-like stem cells (RSCs), a self-renewing naive-primed intermediate. RSCs erase constitutive heterochromatin marks and display a primed chromatin landscape, with bivalently marked primed pluripotency genes. Nonetheless, WNT induces reversion to naive pluripotency. The rosette is therefore a reversible pluripotent intermediate where control over both pluripotency progression and morphogenesis pivots from WNT to MEK signals.

2020-04-28 | GSE112234 | GEO

In vitro capture and characterization of embryonic rosette-stage pluripotency between naive and primed states (I, bulk RNA-Seq data)

Project description:Naive pluripotent cells in the implanting mouse blastocyst generate a rosette structure before undergoing lumenogenesis to form the egg cylinder. Simultaneously, they acquire primed pluripotency, the ability to differentiate into the primary germ layers. The existence of discrete intermediate pluripotent states during this transition has not been demonstrated. We identify here a distinct rosette pluripotent state, defined by co-expression of naive factors with transcription factor OTX2. Downregulation of WNT signals in the blastocyst drives transition into rosette pluripotency by inducing OTX2. The rosette then activates MEK signals that induce lumenogenesis and drive progression to primed pluripotency. Consequently, combined WNT and MEK inhibition supports rosette-like stem cells (RSCs), a self-renewing naive-primed intermediate. RSCs gain a unique epigenome that includes erasure of constitutive heterochromatin and bivalent marking of primed pluripotency genes. Notwithstanding this primed chromatin landscape, WNT induces reversion to naive pluripotency. The rosette is therefore a reversible pluripotent intermediate where control over pluripotency progression and morphogenesis pivots from WNT to MEK signals.

2020-04-28 | GSE105762 | GEO

In vitro capture and characterization of embryonic rosette-stage pluripotency between naive and primed states (II, single-cell RNA-Seq data)

2020-04-28 | GSE145726 | GEO

In vitro capture and characterization of embryonic rosette-stage pluripotency between naive and primed states

Project description:In vitro capture and characterization of embryonic rosette-stage pluripotency between naive and primed states

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In vitro capture and characterization of embryonic rosette-stage pluripotency between naive and primed states

Project description:In vitro capture and characterization of embryonic rosette-stage pluripotency between naive and primed states

| PRJNA608002 | ENA

In vitro capture and characterization of embryonic rosette-stage pluripotency between naive and primed states (II, single-cell RNA-Seq data)

Project description:In vitro capture and characterization of embryonic rosette-stage pluripotency between naive and primed states (II, single-cell RNA-Seq data)

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In vitro capture and characterization of embryonic rosette-stage pluripotency between naive and primed states

Project description:This SuperSeries is composed of the SubSeries listed below. SubSeries GSE105762 contains bulk RNA-Seq data, while SubSeries GSE145726 contains single-cell RNA-Seq data.

2020-04-28 | GSE145727 | GEO

Profiling human naive and primed pluripotent states

Project description:Here we analyse transcriptome profiles of naive, primed and intermediate populations of human pluripotent stem cells

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Characterization of distinct states of human naive pluripotency

Project description:The extent of naive characteriztics of recently reported naive human pluripotent stem cells (hPSCs) obtained in different naive-permissive media, is unclear. Moreover, these naive hPSCs were mainly derived by conversion from primed hPSCs or by direct derivation from human embryos rather than by somatic cell reprogramming. Here, we derived genetically matched human naive hPSCs by direct reprogramming of fibroblasts as well as primed-to-naive conversion using different naive conditions (NHSM, RSeT, 5iLAF and t2iLGöY). Comprehensive characterization showed that naive hPSCs obtained in these different conditions represent a spectrum of naive characteriztics irrespective of whether they were derived by conversion or reprograming. Importantly, only t2iLGöY hPSCs displayed a similar transcriptome to human cells from the inner cell mass, karyotypic stability and require re-priming for trilineage differentiation. Furthermore, our analyses identified KLF4 as a key reprogramming factor which enables conversion of primed hPSCs into naive t2iLGöY hPSCs. These findings underscore the role that reprogramming factors can play for the derivation of bona fide naive hPSCs and provide a molecular and functional reference for all the analysed conditions, which will help accelerate the downstream applications of naive hiPSCs.

2017-09-25 | GSE102851 | GEO

The ETS Transcription Factor ERF Controls the Exit from the Embryonic Rosette-stage of Pluripotency [RRBS]

Project description:The naïve epiblast undergoes a transition to a pluripotent primed state during embryo implantation. Interestingly, a distinct intermediate stage during the naïve-to-primed transition has been recently described, the rosette stage. We propose the transcriptional repressor ERF as the MAPK-dependent switch that controls the exit from the rosette-stage of pluripotency. By using inducible ESC to genetically eliminate all RAS proteins, we show that, while differentiated RasKO ESC are reminiscent of the pluripotent rosette-stage, the absence of ERF overcomes the developmental blockage of RAS-deficient cells from this intermediate state. RNAseq data revealed that deletion of ERF restored the overall gene expression profile to a wild-type level in differentiated RasKO ESC. Mechanistically, ERF ensures naïve pluripotency by strengthening naïve pluripotent transcription factor binding and accessibility at specific ESC enhancers. Moreover, ERF regulates negatively the expression of the DNMT3 de novo methylases, which are essential for the extinction of the naïve transcriptional program. Our data revealed an essential role for ERF in the exit from rosette pluripotency as a regulator of the progression to primed pluripotency.

2021-08-06 | GSE162580 | GEO

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