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Single-cell analysis of bidirectional reprogramming between early embryonic states reveals mechanisms of differential lineage plasticities [ATAC-Seq]

ABSTRACT: Two distinct fates, pluripotent epiblast (EPI) and primitive (extra-embryonic) endoderm (PrE), arise from common progenitor cells, the inner cell mass (ICM), in mammalian embryos. To study how these sister identities are forged, we leveraged embryonic (ES) and eXtraembryonic ENdoderm (XEN) stem cells – in vitro counterparts of the EPI and PrE. Bidirectional reprogramming between ES and XEN coupled with single-cell RNA and ATAC-seq analyses uncovered distinct rates, efficiencies and trajectories of state conversions, identifying drivers and roadblocks of reciprocal conversions. While GATA4-mediated ES-to-iXEN conversion was rapid and nearly deterministic, OCT4, KLF4 and SOX2-induced XEN-to-iPS reprogramming progressed with diminished efficiency and kinetics. The dominant PrE transcriptional program, safeguarded by Gata4, and globally elevated chromatin accessibility of EPI underscored the differential plasticities of the two states. Mapping in vitro trajectories to embryos revealed reprogramming in either direction tracked along, and toggled between, EPI and PrE in vivo states without transitioning through the ICM.

ORGANISM(S): Mus musculus

PROVIDER: GSE266452 | GEO | 2024/08/25

REPOSITORIES: GEO

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Single-cell analysis of bidirectional reprogramming between early embryonic states reveals mechanisms of differential lineage plasticities [scATAC-seq]

Project description:Two distinct lineages, pluripotent epiblast (EPI) and primitive (extra-embryonic) endoderm (PrE), arise from common inner cell mass (ICM) progenitor cells in mammalian embryos. To study how these sister identities are forged, we leveraged embryonic (ES) and eXtraembryonic ENdoderm (XEN) stem cells – in vitro counterparts of the EPI and PrE. Bidirectional reprogramming between ES and XEN coupled with single-cell RNA and ATAC-seq analyses uncovered distinct rates, efficiencies and trajectories of state conversions, identifying drivers and roadblocks of reciprocal conversions. While GATA4-mediated ES-to-iXEN conversion was rapid and nearly deterministic, OCT4, KLF4 and SOX2-induced XEN-to-iPS reprogramming progressed with diminished efficiency and kinetics. A dominant PrE transcriptional program, safeguarded by Gata4, and globally elevated chromatin accessibility of EPI underscored the differential plasticities of the two states. Mapping in vitro to embryo trajectories revealed reprogramming in either direction tracked along, and toggled between, EPI and PrE in vivo states without transitioning through the ICM.

2024-09-09 | GSE276702 | GEO

Single-cell analysis of bidirectional reprogramming between early embryonic states reveals mechanisms of differential lineage plasticities [scRNA-Seq]

2024-09-09 | GSE276704 | GEO

Single-cell analysis of bidirectional reprogramming between early embryonic states reveals mechanisms of differential lineage plasticities [RNA-Seq]

Project description:Two distinct fates, pluripotent epiblast (EPI) and primitive (extra-embryonic) endoderm (PrE), arise from common progenitor cells, the inner cell mass (ICM), in mammalian embryos. To study how these sister identities are forged, we leveraged embryonic (ES) and eXtraembryonic ENdoderm (XEN) stem cells – in vitro counterparts of the EPI and PrE. Bidirectional reprogramming between ES and XEN coupled with single-cell RNA and ATAC-seq analyses uncovered distinct rates, efficiencies and trajectories of state conversions, identifying drivers and roadblocks of reciprocal conversions. While GATA4-mediated ES-to-iXEN conversion was rapid and nearly deterministic, OCT4, KLF4 and SOX2-induced XEN-to-iPS reprogramming progressed with diminished efficiency and kinetics. The dominant PrE transcriptional program, safeguarded by Gata4, and globally elevated chromatin accessibility of EPI underscored the differential plasticities of the two states. Mapping in vitro trajectories to embryos revealed reprogramming in either direction tracked along, and toggled between, EPI and PrE in vivo states without transitioning through the ICM.

2024-08-25 | GSE266451 | GEO

Single-cell analysis of bidirectional reprogramming between early embryonic states reveals mechanisms of differential lineage plasticities [CUT&Run]

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Primitive endoderm stem cell lines in mice

Project description:A blastocyst consists of three distinctive cell types: epiblast (EPI), trophoblast (TB), and primitive endoderm (PrE). Stem cell lines representing EPI and TB (embryonic stem (ES) cells and trophoblast stem (TS) cells) have been derived and they contribute to epiblast derivatives and trophoblast derivatives of stem cell-blastocyst chimeras, respectively. Although derived from PrE, extraembryonic endoderm (XEN) cells contribute to only a limited part of parietal endoderm (PE) but rarely to other PrE derivatives. Here we describe the establishment of primitive endoderm stem (PrES) cell lines in mice. PrES cells were derived and maintained in a serum-free media containing CHIR99021, FGF4, heparin, and PDGF-AA. RNA-seq analysis revealed that the transcriptome of PrES cells is globaly different from XEN cells: PrES cells express not only endoderm markers (Dab2, Gata4, Gata6, Sox17, etc.), but also pluripotent markers (Pou5f1, Cdh1, Nanog, Zfp42, etc.), and resembles in vivo founder PrE. PrES cells were rapidly and efficiently incorporated into PrE after blastocyst injection and efficiently contributed to all PrE derivatives, including PE, VE (visceral endoderm), and MZE (marginal zone endoderm) in chimeras. Importantly, PrES cells rescued embryonic lethality of PrE-depleted blastocysts by complementing all PrE derivatives. PrES cells thus not only contribute to understanding of the mechanisms of PrE specification but also provide a critical resource for artificial embryo reconstitution by stem cells alone.

2020-05-30 | GSE130957 | GEO

Zfp281 functions as a barrier in embryonic stem cells to extraembryonic endoderm stem cells differentiation [RNA-seq]

Project description:Cell-fate decisions and lineage commitment in early embryonic development are governed by comprehensive gene-regulatory programs. However, the molecular details leading to initial segregation of different lineages remain unclear. In the second cell-fate decision, epiblast (EPI) and primitive endoderm (PrE) lineages are formed from the pluripotent inner cell mass (ICM) cells at blastocyst stage. Here, we demonstrated that the pluripotency transcription factor Zfp281 is a barrier in embryonic stem cells (ESCs) to PrE lineage differentiation. Zfp281 is expressed in extraembryonic endoderm cells (XENs), the ex vivo derivatives of PrE. But knockdown of Zfp281 doesn’t affect either maintenance or expression of the PrE master regulators in XENs. Using an in vitro differentiation protocol, we revealed that knockout of Zfp281 significantly increased the efficiency of ESC to XEN derivation. Using a Zfp281 rescue line for the knockout cells, we further confirmed that effects of elevated efficiency of XEN derivation is specifically due to loss of Zfp281. Mechanistically, we revealed that Zfp281 interacts with components in the polycomb repressive complex 2 (PRC2), and recruits PRC2 to promoters of PrE master regulators GATA4 and GATA6 for transcriptional and epigenetic repression. Taken together, our results demonstrated a novel role of Zfp281 in second cell-fate decision in embryonic stem cell differentiation.

2020-08-19 | GSE154398 | GEO

Zfp281 functions as a barrier in embryonic stem cells to extraembryonic endoderm stem cells differentiation [ChIP-seq]

2020-08-19 | GSE148231 | GEO

Cell-to-cell gene expression variability followed by reinforcement progressively segregates lineages in the early mouse embryo

Project description:Mammalian embryonic development begins with the specification and segregation of the two extra-embryonic lineages, trophectoderm and primitive endoderm, from the pluripotent embryonic lineage, the epiblast. To establish a map of epiblast (EPI) versus primitive endoderm (PrE) lineage segregation which occurs within the inner cell mass (ICM), we comprehensively characterised the gene expression profiles of individual inner cells during blastocyst development. Lineage represents the two embryonic cell lineages: the epiblast (EPI), and the primitive endoderm (PE), which are segregated within the inner cell mass(ICM) during blastocyst development.

2013-11-26 | E-MTAB-1681 | biostudies-arrayexpress

Mouse Global gene expression profiles of mouse embryonic day3.75 inner cell mass cells

Project description:The goal of this study is elucidating the mechanisms of the primitive endoderm (PrE, founder of the yolk sac) segregates from the epiblast (EPI, founder of the foetus). Within the uterus and ex vivo, precursors of the EPI and PrE emerge in an unsorted manner in inner cell mass (ICM). Coincident with identity acquisition, the cells physically sort, resulting in PrE establishing a single layer of cells covering the cavity-facing surface of the ICM with the EPI enclosed between the PrE and polar trophectoderm. The mechanism that determines this spatial segregation between EPI and PrE is still poorly understood. To achieve this goal, we have compared mouse embryonic day (E) 3.75 ICM cells’ transcriptome profiling to other existing mouse E3.5 and E4.5 ICM cells’ RNA-seq data. We have identified the timing of EPI and PrE lineages specification and maturation and each stage- and lineage-specific genes expression profiles.

2022-01-09 | GSE148462 | GEO

OCT4 is expressed in extraembryonic endoderm stem (XEN) cell progenitors during somatic cell reprogramming

Project description:During development, progenitors of embryonic stem (ES) and extraembryonic endoderm stem (XEN) cells are concomitantly specified within the inner cell mass (ICM) of the mouse blastocyst. Similarly, XEN cells are induced (iXEN cells) alongside induced pluripotent stem (iPS) cells following overexpression ofOct4,Sox2,Klf4andMyc(OSKM) during somatic cell reprogramming. It is unclear how or why this cocktail produces both stem cell types, but OCT4 has been associated with non-pluripotent outcomes. In this report, we show that, during OSKM reprogramming, many individualOct4-GFP-expressing cells are fated to become iXEN cells. Interestingly, SKM alone was also sufficient to induce iXEN cell formation, likely via activation of endogenousOct4.These observations indicate that iXEN cell formation is not strictly an artifact ofOct4overexpression. Moreover, our results suggest that a pathway to XEN may be an integral feature of establishing pluripotency during reprogramming, as in early embryo development.

2024-02-15 | GSE244818 | GEO

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