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Comprehensive miRNA profiling of human naïve, intermediate and primed pluripotent stem cells

ABSTRACT: Comprehensive miRNA profiling of human naïve, intermediate and primed pluripotent stem cells

PROVIDER: PRJNA526900 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR8723490.fastq.gz	Fastqsanger.gz
	SRR8723500.fastq.gz	Fastqsanger.gz
	SRR8723491.fastq.gz	Fastqsanger.gz
	SRR8723501.fastq.gz	Fastqsanger.gz
	SRR8723492.fastq.gz	Fastqsanger.gz

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Comprehensive miRNA profiling of human naïve, intermediate and primed pluripotent stem cells

Project description:Naïve human pluripotent stem cells (hPSC) represent an earlier time-point in embryogenesis than conventional, ‘primed’ hPSCs. We present a comprehensive miRNA profiling of naïve-to-primed transition in hPSC, a process resembling aspects of early in vivo embryogenesis. We identify miR-143-3p and miR-22-3p as markers of the naïve state and miR-363-5p, several members of the miR-17 family, miR-302 family as primed markers. We uncover that miR-371-373 are highly upregulated in naïve hPSC. MiR-371-373 are the human homologs of the mouse miR-290 family, which are the most highly expressed miRNAs in mPSC. This aligns with the consensus that naïve hPSC resemble mPSC, showing that the absence of miR-371-373 in conventional hPSC is due to cell state rather than a species difference.

2020-06-29 | GSE128260 | GEO

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Chromatin accessibility analysis of intermediates during human primed and naïve reprogramming.

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An Intermediate Pluripotent State Controlled by microRNAs is Required for the Naïve to Primed Stem Cell Transition

Project description:An Intermediate Pluripotent State Controlled by microRNAs is Required for the Naïve to Primed Stem Cell Transition

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SMAD2/3 chromatin immunoprecipitation sequencing (ChIP-seq) in human naïve and primed human pluripotent stem cells

Project description:The aim of this experiment was to investigate the role of TGFβ signalling pathway in human pluripotency, through ChIP-seq analysis of its main downstream effector SMAD2/3 in naïve and primed human pluripotent stem cells (hPSCs).

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Project description:We derived primed pluripotent stem cell cultures (PSCs) from marmoset blastocyst using conventional human PSC culture conditions (KSR/bFGF on feeders). Naïve marmoset PSCs were established by chemical resetting. In addition, we generated forebrain-derived cells from the frontal lobe of a marmoset neonate. Individual cells were manually isolated with a mouth pipette and subjected to single-cell full-lengths transcriptome profiling using a modified version of Smart-Seq2.

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An Intermediate Pluripotent State Controlled by microRNAs is Required for the Naïve to Primed Stem Cell Transition

Project description:The embryonic stem cell (ESC) transition from naive to primed pluripotency is marked by major changes in cellular properties and developmental potential. ISY1 is implicated in miRNA biogenesis yet its widespread role and relevance to ESC biology remain unknown. Here we find that highly dynamic ISY1 expression during the naïve to primed ESC transition defines a unique phase of ‘poised’ pluripotency characterized by distinct miRNA and mRNA transcriptomes and widespread poised cell contribution to mouse chimeras. Loss- and gain-of-function experiments reveal that ISY1 promotes exit from the naïve state, is necessary and sufficient to induce and maintain poised pluripotency, and that persistent ISY1 overexpression inhibits the transition from the naïve to the primed state. We identify a large subset of ISY1-dependent miRNAs that can rescue the inability of miRNA-deficient ESCs to establish the poised state and transition to the primed state. Thus, dynamic ISY1 regulates poised pluripotency through miRNAs to control ESC fate.

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Project description:Defining how human pluripotent cell identity is controlled and in particular how naïve pluripotency is acquired during cell reprogramming is crucial for the future applications of pluripotent stem cells. However, the regulatory pathways of naïve cell reprogramming remain incompletely understood. Here, we used genome-wide CRISPR-Cas9 screening to identify novel regulators of primed to naïve pluripotent stem cell reprogramming, including genes that are essential for reprogramming and genes that normally impede reprogramming and whose targeted deletion led to enhanced reprogramming. Integrated analysis defined specific chromatin complexes and signalling pathways as critical regulators of naïve reprogramming, and were largely distinct from regulators of somatic cell reprogramming. Mechanistically, PRC1.3 and PRDM14 are jointly required to transcriptionally repress developmental and gene regulatory factors to ensure naïve cell reprogramming. Additionally, small molecule inhibitors of reprogramming impediments increased the efficiency of naïve cell reprogramming, and are of practical benefit that can improve on current reprogramming methods. Taken together, we have identified novel regulators controlling the establishment of naïve pluripotency in human cells, which will open up new ways to exploit the full potential of pluripotent stem cells. These results also provide new insights into mechanisms that destabilise and reconfigure cell identity during cell state transitions.

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