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Cell fate roadmap with pre-implantation lineage signatures during primed-to-naive transition process

ABSTRACT: Cell fate roadmap with pre-implantation lineage signatures during primed-to-naive transition process

PROVIDER: PRJNA728461 | ENA |

REPOSITORIES: ENA

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Cell fate roadmap with pre-implantation lineage signatures during primed-to-naive transition process

Project description:We describe the global cell roadmap during primed-to-naive transition process in single-cell level by performing integrated scRNA-seq analysis between primed, day 6, day 8, day 10, day14 and naïve (10× genomics)scRNA-seq libraries generated in this study.

2022-04-26 | GSE173756 | GEO

Cell fate roadmap of human primed-to-naive transition reveals preimplantation cell lineage signatures

Project description:We describe the global cell fate roadmap during primed-to-naive transition process by bulk mRNA-seq and ATAC-seq analysis among transition intermediates across different time points. We report that activation of ALPG is a landmark event for naive state establishment. Further investigation into transitioning cells with dynamic fluorescence presents intermediates branching into TE-like subpopulations with capacities of TSC derivation.

2022-04-29 | GSE174771 | GEO

A rewiring of DNA replication mediated by MRE11 exonuclease underlies primed-to-naive cell de-differentiation

Project description:Mouse embryonic stem cells (mESCs) in the primed pluripotency state, that resembles the post-implantation epiblast, can be de-differentiated in culture to anaivestate that resembles the pre-implantation inner cell mass.We report that primed-to-naive mESC transition entails a significant slowdown of DNA replication forks and the compensatory activation of dormant origins. Using iPOND (“isolation of proteins on nascent DNA”) coupled to mass spectrometry, we identify key changes in replisome composition that are responsible for these effects. Naive mESC forks are enriched in MRE11 nuclease and other DNA repair proteins. MRE11 is recruited to newly synthesized DNA in response to transcription-replication conflicts, and its inhibition or genetic downregulation in naive mESCs is sufficient to restore the fork speed observed in primed cells. Notably, MRE11 is required for the efficient primed-to-naive mESC transition, demonstrating a direct link between DNA replication dynamics and the mESC de-differentiation process

2024-04-03 | GSE254126 | GEO

Cell fate roadmap of human primed-to-naive transition reveals preimplantation cell lineage signatures

Project description:Cell fate roadmap of human primed-to-naive transition reveals preimplantation cell lineage signatures

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Naive Pluripotent Stem Cells Display Transcriptional and Epigenetic Signatures of the Human Pre-Implantation Embryo

Project description:Significant interest has been devoted to the isolation of human pluripotent stem cells displaying the naive state of mouse embryonic stem cells. However, to what extent naive human cells isolated in culture resemble pluripotent cells in vivo remains unclear. Here we present three lines of evidence indicating that naive pluripotent stem cells generated in the absence of transgenes share defining molecular signatures with the human pre-implantation embryo. First, a comprehensive analysis of the transposcriptome reveals that naive human cells have a retroelement expression profile of human cleavage stage embryos. Second, base-resolution mapping of the DNA methylome in naive human cells reveals a genome-wide reduction in CpG and non-CpG methylation levels. Third, female naive cells exhibit an X chromosome status that is similar to that of the human blastocyst. Our work demonstrates that pluripotent stem cells with epigenomic hallmarks of the early human embryo can be directly captured in vitro. Examine the methylomes of 6 naÃ¯ve, 2 primed and 2 re-primed human embryonic stem cells

2016-07-18 | E-GEOD-75868 | biostudies-arrayexpress

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

RNA-seq of naive and primed ES cells

Project description:Here we propose a set of molecular criteria for evaluating the naive human pluripotent state. We show by RNA-seq that transcription of transposable elements provides a sensitive measure of the concordance between pluripotent stem cells and early human development. RNA-seq of 4 naive ES samples in 4i/LA, 3 naive ES samples in 5i/LA, 2 transgene-dependant naive ES cell samples, and 5 primed ES cell samples (in hESM)

2016-07-15 | E-GEOD-83765 | biostudies-arrayexpress

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

2017-03-23 | GSE93241 | GEO

Changes in replisome composition underlie the rewiring of DNA replication during embryonic stem cell reprogramming

Project description:Pluripotent stem cells can give rise to the three embryonic germ layers and the characterization of their properties is crucial to exploit their therapeutic potential. Mouse embryonic stem cells (mESCs) are isolated and usually maintained in vitro in a primed state that resembles the post-implantation epiblast features. Furthermore, primed mESCs can be de-differentiated to a naive state that resembles the pre-implantation inner cell mass (ICM). Cell differentiation or genotoxic stress, among others, can alter DNA replication, which is a flexible process able to adapt to different cellular contexts. Here, we demonstrate that primed-to-naive mESC reprogramming triggers replication fork slowdown, increased fork asymmetry and a compensatory activation of dormant origins. Using iPOND (“isolation of proteins on nascent DNA”) coupled to mass spectrometry we have characterized the changes in replisome composition between naive and primed mESCs. Several DNA repair factors, including MRE11 nuclease, are enriched in naive mESCs forks, while factors involved in ubiquitin-dependent protein metabolism are enriched in primed mESC forks. We report that primed-to-naive mESC de-differentiation promotes recruitment of MRE11 to the forks in response to transcription-replication conflicts, underlying the DNA replication rewiring required for efficient mESC reprogramming.

2024-04-03 | PXD041946 | Pride

RNA-seq of naive and primed ES cells (NHSM)

Project description:Here we propose a set of molecular criteria for evaluating the naive human pluripotent state. We show by RNA-seq that transcription of transposable elements provides a sensitive measure of the concordance between pluripotent stem cells and early human development. RNA-seq of 3 naive ES samples in NHSM (Gafni et al.) and 3 primed ES cell samples (in hESM)

2016-08-16 | E-GEOD-85689 | biostudies-arrayexpress

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