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Probing the signaling requirements for naïve human pluripotency by high-throughput chemical screening [WGBS]

ABSTRACT: Probing the signaling requirements for naïve human pluripotency by high-throughput chemical screening [WGBS]

PROVIDER: PRJNA641790 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR12088431_1.fastq.gz	Fastqsanger.gz
	SRR12088431_2.fastq.gz	Fastqsanger.gz
	SRR12088432_1.fastq.gz	Fastqsanger.gz
	SRR12088432_2.fastq.gz	Fastqsanger.gz
	SRR12088433_1.fastq.gz	Fastqsanger.gz

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Probing the signaling requirements for naïve human pluripotency by high-throughput chemical screening [WGBS]

Project description:Background: Naïve human embryonic stem cells (hESCs) have been isolated that more closely resemble the pre-implantation epiblast compared to conventional “primed” hESCs, but the signaling principles underlying these discrete stem cell states remain incompletely understood. Methods:Here we performed high-throughput screening using a library of >3,000 well-annotated compounds to identify essential signaling requirements for naïve human pluripotency. Results:We report that MEK1/2 inhibitors can be replaced during maintenance of naïve human pluripotency by inhibitors targeting either upstream (FGFR, RAF1) or downstream (ERK1/2) kinases. Naïve hESCs maintained under these alternative conditions display elevated levels of ERK phosphorylation but retain genome-wide DNA hypomethylation and a transcriptional identity of the pre-implantation epiblast. In contrast, dual inhibition of MEK and ERK promotes efficient primed-to-naïve resetting in combination with PKC, ROCK, and TNKS inhibitors and Activin A. Conclusions: This work demonstrates that induction and maintenance of naïve human pluripotency are governed by distinct signaling requirements.

2021-06-15 | GSE153213 | GEO

Probing the signaling requirements for naïve human pluripotency by high-throughput chemical screening

Project description:Probing the signaling requirements for naïve human pluripotency by high-throughput chemical screening

| PRJNA641786 | ENA

Probing the signaling requirements for naïve human pluripotency by high-throughput chemical screening [RNA-seq]

2021-06-15 | GSE153212 | GEO

Probing the signaling requirements for naïve human pluripotency by high-throughput chemical screening [RNA-seq]

Project description:Probing the signaling requirements for naïve human pluripotency by high-throughput chemical screening [RNA-seq]

| PRJNA641789 | ENA

Probing the signaling requirements for naïve human pluripotency by high-throughput chemical screening

Project description:This SuperSeries is composed of the SubSeries listed below.

2021-06-15 | GSE153215 | GEO

Principles of Signalling Pathway Modulation for Enhancing Human Naïve Pluripotency Induction [WGBS]

Project description:Isolating human MEK/ERK signalling independent pluripotent stem cells (PSCs) with characteristics of naive pluripotency while maintaining differentiation competence and genetic integrity, remains challenging. Here we engineer reporter systems that allow screening for conditions that induce molecular and functional features of human naive pluripotency. Synergistic inhibition of WNT-ßCATENIN, PKC and SRC signalling enables induction of teratoma competent naïve human PSCs, with capacity to differentiate into trophoblast stem cells (TSC) and extraembryonic endodermal (XEN) cells in vitro. Divergent signalling and transcriptional requirements for boosting naïve pluripotency were found between mouse and human. P53 depletion in human naïve PSCs endows them with competitiveness to better contribute to mouse-human cross-species chimeric embryos upon priming. Finally, MEK/ERK inhibition can be substituted with inhibition for NOTCH/RBPj, which allows inducing alternative human naïve-like PSCs with diminished risk for deleterious global DNA hypomethylation. Our findings set a framework for defining the signalling foundations of human naïve pluripotency.

2021-03-25 | GSE142812 | GEO

Probing the signaling requirements for naive human pluripotency by high-throughput chemical screening.

Project description:Naive human embryonic stem cells (hESCs) have been isolated that more closely resemble the pre-implantation epiblast compared to conventional "primed" hESCs, but the signaling principles underlying these discrete stem cell states remain incompletely understood. Here, we describe the results from a high-throughput screen using ∼3,000 well-annotated compounds to identify essential signaling requirements for naive human pluripotency. We report that MEK1/2 inhibitors can be replaced during maintenance of naive human pluripotency by inhibitors targeting either upstream (FGFR, RAF) or downstream (ERK1/2) kinases. Naive hESCs maintained under these alternative conditions display elevated levels of ERK phosphorylation but retain genome-wide DNA hypomethylation and a transcriptional identity of the pre-implantation epiblast. In contrast, dual inhibition of MEK and ERK promotes efficient primed-to-naive resetting in combination with PKC, ROCK, and TNKS inhibitors and activin A. This work demonstrates that induction and maintenance of naive human pluripotency are governed by distinct signaling requirements.

| S-EPMC8272458 | biostudies-literature

Principles of Signalling Pathway Modulation for Enhancing Human Naïve Pluripotency Induction [WGBS]

Project description:Principles of Signalling Pathway Modulation for Enhancing Human Naïve Pluripotency Induction [WGBS]

| PRJNA598429 | ENA

Inflammation switches the chemoattractant requirements for naïve lymphocyte entry into lymph nodes

Project description:Inflammation switches the chemoattractant requirements for naïve lymphocyte entry into lymph nodes

| PRJNA1185220 | ENA

Carbodiimide reagents for the chemical probing of RNA structure in cells

Project description:Deciphering the conformations of RNAs in their cellular environment allows identification of RNA elements with potentially functional roles within biological contexts. Insight into the conformation of RNA in cells has been achieved using chemical probes that were developed to react specifically with flexible RNA nucleotides, or the Watson-Crick face of single-stranded nucleotides. The most widely used probes are either selective SHAPE (2'-hydroxyl acylation and primer extension) reagents that probe nucleotide flexibility, or dimethyl sulfate (DMS), which probes the base-pairing at adenine and cytosine but is unable to interrogate guanine or uracil. The constitutively charged carbodiimide N-cyclohexyl-N'-(2-morpholinoethyl)carbodiimide metho-p-toluenesulfonate (CMC) is widely used for probing G and U nucleotides, but has not been established for probing RNA in cells. Here, we report the use of a smaller and conditionally charged reagent, 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC), as a chemical probe of RNA conformation, and the first reagent validated for structure probing of unpaired G and U nucleotides in intact cells. We showed that EDC demonstrates similar reactivity to CMC when probing transcripts in vitro. We found that EDC specifically reacted with accessible nucleotides in the 7SK noncoding RNA in intact cells. We probed structured regions within the Xist lncRNA with EDC and integrated these data with DMS probing data. Together, EDC and DMS allowed us to refine predicted structure models for the 3’ extension of repeat C within Xist. These results highlight how complementing DMS probing experiments with EDC allows the analysis of Watson-Crick base-pairing at all four nucleotides of RNAs in their cellular context.

2018-12-26 | GSE118309 | GEO

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