Formative transition of human naïve pluripotent stem cells
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA507424 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR8257120.fastq.gz | Fastqsanger.gz | |||
| SRR8257130.fastq.gz | Fastqsanger.gz | |||
| SRR8257140.fastq.gz | Fastqsanger.gz | |||
| SRR8257150.fastq.gz | Fastqsanger.gz | |||
| SRR8257160.fastq.gz | Fastqsanger.gz |
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Project description:Human naïve pluripotent stem cells (PSC) share features with pre-implantation epiblast. They thus provide an unmatched opportunity for characterising the developmental programme of pluripotency in Homo sapiens. Here we confirm that naïve PSC do not respond directly to germ layer induction, but must first acquire competence. Capacitation for multi-lineage differentiation occurs without exogenous growth factor stimulation and is facilitated by inhibition of Wnt signalling. Whole transcriptome profiling during this formative transition highlights dynamic changes in gene expression, affecting many cellular properties, including metabolism and epithelialisation. Notably, naïve pluripotency factors are exchanged for post-implantation factors, but competent cells remain devoid of lineage primed transcription. The gradual pace of transition for human naïve PSC is consistent with the timespan of primate development from blastocyst to gastrulation. Transcriptome trajectory during in vitro capacitation of human naïve cells tracks the progression of epiblast during embryogenesis in Macaca fascicularis, but shows greater divergence from mouse development. Thus the formative transition of naïve PSC in a simple culture system may recapitulate essential and specific features of pluripotency dynamics during an inaccessible period of human embryogenesis.
2019-03-07 | GSE123055 | GEO
Project description:The transition of mammalian early epiblast at different phases is characterized by the differences of pluripotent states and developmental potential, involving extensive transcriptome changes. However, the role of post-transcriptional RNA degradation modulation in cell fate transition remains largely unexplored. Here, we report that deadenylase Cnot8 of Ccr4-Not complex specifically plays a role in naïve-to-formative transition of pluripotent stem cells (PSCs). Disruption of Cnot8 results in early embryonic lethality, accompanying with the increased expression levels of naïve transcription factors in mouse epiblasts. Cnot8 depletion leads to accumulated expression abundances and increased poly(A) tail lengths of massive transcripts including mRNAs of naïve regulation networks, impairing the naïve-to-formative pluripotency conversion. Mechanistically, Cnot8 interacts with Tob1 and Pabpc1 to guarantee the prompt mRNA deadenylation and degradation of naïve regulation networks at specific time. Together, these findings delineate the mechanism underlying PSC fate transition through global degradation of mRNAs for naïve regulation networks by Cnot8.
2022-05-11 | GSE194431 | GEO
Project description:The transition of mammalian early epiblast at different phases is characterized by the differences of pluripotent states and developmental potential, involving extensive transcriptome changes. However, the role of post-transcriptional RNA degradation modulation in cell fate transition remains largely unexplored. Here, we report that deadenylase Cnot8 of Ccr4-Not complex specifically plays a role in naïve-to-formative transition of pluripotent stem cells (PSCs). Disruption of Cnot8 results in early embryonic lethality, accompanying with the increased expression levels of naïve transcription factors in mouse epiblasts. Cnot8 depletion leads to accumulated expression abundances and increased poly(A) tail lengths of massive transcripts including mRNAs of naïve regulation networks, impairing the naïve-to-formative pluripotency conversion. Mechanistically, Cnot8 interacts with Tob1 and Pabpc1 to guarantee the prompt mRNA deadenylation and degradation of naïve regulation networks at specific time. Together, these findings delineate the mechanism underlying PSC fate transition through global degradation of mRNAs for naïve regulation networks by Cnot8.
2022-05-11 | GSE174424 | GEO
Project description:The transition of mammalian early epiblast at different phases is characterized by the differences of pluripotent states and developmental potential, involving extensive transcriptome changes. However, the role of post-transcriptional RNA degradation modulation in cell fate transition remains largely unexplored. Here, we report that deadenylase Cnot8 of Ccr4-Not complex specifically plays a role in naïve-to-formative transition of pluripotent stem cells (PSCs). Disruption of Cnot8 results in early embryonic lethality, accompanying with the increased expression levels of naïve transcription factors in mouse epiblasts. Cnot8 depletion leads to accumulated expression abundances and increased poly(A) tail lengths of massive transcripts including mRNAs of naïve regulation networks, impairing the naïve-to-formative pluripotency conversion. Mechanistically, Cnot8 interacts with Tob1 and Pabpc1 to guarantee the prompt mRNA deadenylation and degradation of naïve regulation networks at specific time. Together, these findings delineate the mechanism underlying PSC fate transition through global degradation of mRNAs for naïve regulation networks by Cnot8.
2022-05-11 | GSE174423 | GEO
Project description:Cnot8 Eliminates Naïve Regulation Networks and Is Essential for Naïve-to-Formative Pluripotent Transition
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Project description:In the mammalian embryo, epiblast cells must exit the naïve state and acquire formative pluripotency. This cell state transition is recapitulated by mouse embryonic stem cells (ESCs), which undergo pluripotency progression in defined conditions in vitro. However, our understanding of the molecular cascades and gene networks involved in the exit from naïve pluripotency remains fragmentary. Here, we employed a combination of genetic screens in haploid ESCs, CRISPR/Cas9 gene disruption, large-scale transcriptomics and computational systems biology to delineate the regulatory circuits governing naïve state exit. Transcriptome profiles for 73 ESC lines deficient for regulators of the exit from naïve pluripotency predominantly manifest delays on the trajectory from naïve to formative epiblast. We find that gene networks operative in ESCs are also active during transition from pre- to post-implantation epiblast in utero. We identified 496 naïve state-associated genes tightly connected to the in vivo epiblast state transition and largely conserved in primate embryos. Integrated analysis of mutant transcriptomes revealed funnelling of multiple gene activities into discrete regulatory modules. Finally, we delineate how intersections with signalling pathways direct this pivotal mammalian cell state transition.
2020-12-22 | GSE145653 | GEO
Project description:Two phases of pluripotency, naïve and primed, have been captured in vitro and studied in details1. A third formative phase was recently proposed to exist between naïve and primed phases2. Formative pluripotency entails permissiveness for direct primordial germ cell (PGC) induction and competence for blastocyst chimeras, and is characterized by transcriptional and epigenetic features intermediate of naïve and primed pluripotency. To date, however, stable pluripotent stem cells (PSCs) harboring formative features haven’t been derived from early mammalian embryos. Here we develop a method which enabled the derivation and culture of stable formative-like embryonic stem cells (ESCs) from mouse blastocysts. Formative-like mouse ESCs share molecular features characteristic of early post-implantation epiblasts and are competent for PGC-like cell induction and blastocyst chimera formation. The same culture also supported the derivation of ESCs and transgene-free induced pluripotent stem cells (iPSCs) from horse blastocysts and fibroblasts, respectively. Horse ESCs/iPSCs transcriptionally resembled mouse formative cells, and could also be directly induced into PGC-like cells. Formative-like horse iPSCs could efficiently chimerize horse, mouse, goat, sheep and pig embryos. Stable formative-like PSCs will be invaluable for studying mammalian pluripotency, and our method may be broadly applicable for the derivation of PGC and chimera competent PSCs from other mammalian species.
2020-11-27 | GSE135990 | GEO
Project description:Two phases of pluripotency, naïve and primed, have been captured in vitro and studied in details1. A third formative phase was recently proposed to exist between naïve and primed phases2. Formative pluripotency entails permissiveness for direct primordial germ cell (PGC) induction and competence for blastocyst chimeras, and is characterized by transcriptional and epigenetic features intermediate of naïve and primed pluripotency. To date, however, stable pluripotent stem cells (PSCs) harboring formative features haven’t been derived from early mammalian embryos. Here we develop a method which enabled the derivation and culture of stable formative-like embryonic stem cells (ESCs) from mouse blastocysts. Formative-like mouse ESCs share molecular features characteristic of early post-implantation epiblasts and are competent for PGC-like cell induction and blastocyst chimera formation. The same culture also supported the derivation of ESCs and transgene-free induced pluripotent stem cells (iPSCs) from horse blastocysts and fibroblasts, respectively. Horse ESCs/iPSCs transcriptionally resembled mouse formative cells, and could also be directly induced into PGC-like cells. Formative-like horse iPSCs could efficiently chimerize horse, mouse, goat, sheep and pig embryos. Stable formative-like PSCs will be invaluable for studying mammalian pluripotency, and our method may be broadly applicable for the derivation of PGC and chimera competent PSCs from other mammalian species.
2020-11-27 | GSE135989 | GEO
Project description:The gene regulatory network in naïve mouse embryonic stem cells (ESC) is reconfigured to enable lineage commitment. Tcf3 sanctions rewiring to formative pluripotency by suppressing components of the ESC transcription factor circuitry. However, Tcf3 depletion only delays, and does not prevent transition. Here we delineate major contributions of Ets-family transcription factor Etv5 and the repressor Rbpj. ERK signalling triggers genome relocation of Etv5 to commission formative pluripotency enhancers. Concomitant up-regulation of Rbpj prevents reversion by repressing potent naïve factors, Nanog and Tbx3. Triple deletion of Etv5, Rbpj and Tcf3 disables naïve ESC, such that they remain undifferentiated and locked in self-renewal even in the presence of differentiation stimuli. Thus, pluripotency dynamics are driven by combined action of two repressors that respectively dissolve and extinguish the naive network, and an activator that initiates transcription of formative network genes. Similar tripartite modality might be a general requirement for robust cell state transitions.
2019-05-09 | GSE122239 | GEO
Project description:Cooperative genetic networks drive embryonic stem cell transition from naïve to formative pluripotency
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