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YAP contributes to DNA methylation remodeling upon mouse embryonic stem cell differentiation

ABSTRACT: YAP contributes to DNA methylation remodeling upon mouse embryonic stem cell differentiation

PROVIDER: PRJNA662507 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR12616347_1.fastq.gz	Fastqsanger.gz
	SRR12616347_2.fastq.gz	Fastqsanger.gz
	SRR12616348_1.fastq.gz	Fastqsanger.gz
	SRR12616348_2.fastq.gz	Fastqsanger.gz
	SRR12616349_1.fastq.gz	Fastqsanger.gz

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YAP contributes to DNA methylation remodeling upon mouse embryonic stem cell differentiation.

Project description:The Yes-associated protein (YAP), one of the major effectors of the Hippo pathway together with its related protein WW-domain-containing transcription regulator 1 (WWTR1; also known as TAZ), mediates a range of cellular processes from proliferation and death to morphogenesis. YAP and WW-domain-containing transcription regulator 1 (WWTR1; also known as TAZ) regulate a large number of target genes, acting as coactivators of DNA-binding transcription factors or as negative regulators of transcription by interacting with the nucleosome remodeling and histone deacetylase complexes. YAP is expressed in self-renewing embryonic stem cells (ESCs), although it is still debated whether it plays any crucial roles in the control of either stemness or differentiation. Here we show that the transient downregulation of YAP in mouse ESCs perturbs cellular homeostasis, leading to the inability to differentiate properly. Bisulfite genomic sequencing revealed that this transient knockdown caused a genome-wide alteration of the DNA methylation remodeling that takes place during the early steps of differentiation, suggesting that the phenotype we observed might be due to the dysregulation of some of the mechanisms involved in regulation of ESC exit from pluripotency. By gene expression analysis, we identified two molecules that could have a role in the altered genome-wide methylation profile: the long noncoding RNA ephemeron, whose rapid upregulation is crucial for the transition of ESCs into epiblast, and the methyltransferase-like protein Dnmt3l, which, during the embryo development, cooperates with Dnmt3a and Dnmt3b to contribute to the de novo DNA methylation that governs early steps of ESC differentiation. These data suggest a new role for YAP in the governance of the epigenetic dynamics of exit from pluripotency.

| S-EPMC7948423 | biostudies-literature

Analysis of hippo pathway upon YAP knockdown and MEK inhibition

Project description:This experiment analyzes the global proteome and phosphoproteome in YAP amplified cell lines upon YAP knockdown and/or MEK inhibition.

2020-03-17 | MSV000085111 | MassIVE

Expression profile of mouse embryonic stem cells upon knockdown or overexpression of YAP

Project description:Expression profile of mouse embryonic stem cells upon knockdown or overexpression of YAP

| PRJNA662512 | ENA

RNA-Seq of DU145 cell line upon knockdown of YAP, TAZ, or YAP/TAZ

Project description:Transcriptome analysis of prostate cancer patient derived organoid DU145 cell line upon knockdown of YAP, TAZ, or YAP/TAZ mediated by siRNAs

2022-03-24 | GSE199347 | GEO

YAP contributes to DNA methylation remodeling upon mouse embryonic stem cell differentiation

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

2020-12-08 | GSE157707 | GEO

RNA-Seq of MSK-PCa3 prostate cancer organoids upon knockdown of FOSL1, YAP, TAZ, or YAP/TAZ

Project description:Transcriptome analysis of prostate cancer patient derived organoid MKS-PCa3 upon knockdown of FOSL1, YAP, TAZ, or YAP/TAZ mediated by siRNAs

2022-02-20 | GSE196813 | GEO

Methylation pattern profile of mouse embryonic stem cells upon knockdown of YAP, during neuroectodermal differentiation

Project description:Methylation pattern profile of mouse embryonic stem cells upon knockdown of YAP, during neuroectodermal differentiation

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Arp2/3 Complex Activity Enables Nuclear YAP for Naïve Pluripotency of Human Embryonic Stem Cells

Project description:Our understanding of transitions of human embryonic stem cells between distinct stages of pluripotency relies predominantly on regulation by transcriptional and epigenetic programs with limited insight on the role of established morphological changes. We report remodeling of the actin cytoskeleton of human embryonic stem cells (hESCs) as they transition from primed to naïve pluripotency that includes assembly of a ring of contractile actin filaments encapsulating colonies of naïve hESCs. Activity of the Arp2/3 complex is required for the actin ring, uniform cell mechanics within naïve colonies, nuclear translocation of the Hippo pathway effectors YAP and TAZ, and effective transition to naïve pluripotency. RNA-sequencing analysis confirms that Arp2/3 complex activity regulates Hippo signaling in hESCs, and impaired naïve pluripotency with inhibited Arp2/3 complex activity is rescued by expressing a constitutively active, nuclear-localized YAP-S127A. Moreover, expression of YAP-S127A partially restored in actin filament fence with Arp2/3 complex inhibition, suggesting that actin filament remodeling is both upstream and downstream of YAP activity. These new findings on the cell biology of hESCs reveal a mechanism for cytoskeletal dynamics coordinating cell mechanics to regulate gene expression and facilitate transitions between pluripotency states.

2024-09-11 | GSE276968 | GEO

Methylation pattern profile of mouse embryonic stem cells upon knockdown of YAP, during neuroectodermal differentiation

Project description:We analyzed by BS-seq the methylation pattern of CTR and YAP knockdown cells in undifferentiated (T0) embryonic stem cells (ESCs) vs cells differentiated toward neuroectodermal fate at day 4 of differentiation (T4). Two biological duplicates for each condition.

2020-12-08 | GSE157704 | GEO

Expression profile of mouse embryonic stem cells upon knockdown or overexpression of YAP

Project description:We looked at the expression profiles of embyonic stem cells (ESCs) 48 hours after YAP siRNAs transfection, to knockdown YAP expression, or after pCAG-YAP transfection, to over-express YAP protein. Total RNA was isolated from three independent experiments and analyzed by RNA-seq.

2020-12-08 | GSE157706 | GEO

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