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Cpt1a drives lipid remodeling in primed-to-naïve pluripotency transition [CUT&Tag]

ABSTRACT: Cpt1a drives lipid remodeling in primed-to-naïve pluripotency transition [CUT&Tag]

PROVIDER: PRJNA1064115 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR27533693_1.fastq.gz	Fastqsanger.gz
	SRR27533693_2.fastq.gz	Fastqsanger.gz
	SRR27533694_1.fastq.gz	Fastqsanger.gz
	SRR27533694_2.fastq.gz	Fastqsanger.gz
	SRR27533695_1.fastq.gz	Fastqsanger.gz

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Cpt1a drives lipid remodeling in primed-to-naïve pluripotency transition

Project description:Cpt1a drives lipid remodeling in primed-to-naïve pluripotency transition

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Cpt1a drives lipid remodeling in primed-to-naïve pluripotency transition [RNA-Seq 2]

Project description:Cpt1a drives lipid remodeling in primed-to-naïve pluripotency transition [RNA-Seq 2]

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Cpt1a drives lipid remodeling in primed-to-naïve pluripotency transition [RNA-Seq 1]

Project description:Cpt1a drives lipid remodeling in primed-to-naïve pluripotency transition [RNA-Seq 1]

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Cpt1a drives lipid remodeling in primed-to-naïve pluripotency transition [CUT&Tag]

Project description:This study aimed at investigating the transciptional changes during transition. What is more, we could look for key metabolic genes regulating transitions.

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The translational landscape of naïve and primed state pluripotency

Project description:Translational control plays a central role in regulation of gene expression and can lead to significant divergence between mRNA- and protein-abundance. The translational landscape of early mammalian development and its impact on cellular proteome, however, remains largely un-explored. Here we used genome-wide approaches combined with time-course analysis to measure the mRNA-abundance, mRNA-translation rate and protein expression during the transition of naïve into primed embryonic stem cells (ESCs). We found that the ground state ESCs cultured with GSK3- and MEK-inhibitors and LIF (2iL) display higher ribosome density on a selective set of mRNAs. These mRNAs show reduced translation during the exit from ground state pluripotency and transition to serum/LIF (SL) culture or upon commitment to primed epiblast-like stem cells (EpiLSCs). Strikingly, integrative analysis with cellular proteome indicate a strong translational buffering of this set of mRNAs in 2iL-ESCs leading to stable protein expression levels. Our data reveal that the global alteration of cellular proteome is largely accompanied by transcriptional rewiring. Furthermore, we identified a set of genes (including UHRF1 and KRAS) that undergo selective post-translational regulation during the transition of naïve into primed pluripotency and linked the observed changes to upstream GSK- and MEK/MAPK-signaling pathways using single inhibitor treated ESCs. Thus, we provide a comprehensive and detailed overview of the global changes in gene expression during the transition of naïve to primed pluripotency and dissect the relative contributions of RNA-transcription, translation and regulation of protein stability in controlling protein abundance.

2020-04-03 | PXD014528 | Pride

Cpt1a drives Lipid remodeling in Primed-to-Naïve Pluripotency Transition

Project description:Intermediate cells induced until Day 3 were collected for proteomic profiling. Concurrently, the acetylation levels of peptides were relatively quantified and analyzed. This involved assessing the extent of acetylation on peptide segments and providing insights into post-translational modifications. The experimental procedure included sample preparation, mass spectrometry analysis, and subsequent data interpretation to understand the cellular protein landscape and acetylation patterns comprehensively.

2024-01-23 | PXD048820 |

Cpt1a drives lipid remodeling in primed-to-naïve pluripotency transition

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

2024-09-05 | GSE253147 | GEO

Reorganization of enhancer patterns in transition from naïve to primed pluripotency (RNA-seq)

Project description:Naïve and primed pluripotency is characterized by distinct signaling requirements, transcriptomes and developmental properties, but both cellular states share key transcriptional regulators, Oct4, Sox2 and Nanog. Here we demonstrate that transition between these two pluripotent states is associated with widespread Oct4 relocalization, mirrored by global rearrangement of enhancer chromatin landscapes. Our genomic and biochemical analyses identified candidate mediators of primed state-specific Oct4 binding, including Otx2 and Zic2/3. Even in the absence of other differentiation cues, premature Otx2 overexpression is sufficient to exit the naïve state, induce transcription of a large subset of primed pluripotency-associated genes and redirect Oct4 to thousands of previously inaccessible sites. However, ability of Otx2 to engage new enhancer regions is determined by its levels, cis-encoded properties of the sites and signaling environment. Our results illuminate regulatory mechanisms underlying pluripotency and suggest that capacity of transcription factors such as Otx2 and Oct4 to function as pioneers is highly context-dependent transcription profile of ESCs and EpiLCs to analzye changes during differentiation and the effect of Otx2 loss and overexpression on the differentiation properties

2014-06-05 | E-GEOD-56096 | biostudies-arrayexpress

Translational and Post-translational LC-MS of Naïve and Primed hESCs

Project description:Deciphering the regulatory network for human naïve and primed pluripotency is of fundamental theoretical and applicable significance. Here, by combining quantitative proteomics, phosphoproteomics and acetylproteomics analyses, we revealed RNA processing and translation as the most differentially-regulated processes between naïve and primed human embryonic stem cells (hESCs). While glycolytic primed hESCs rely predominantly on eIF4E-mediated cap-dependent pathway for protein translation, naïve hESCs with reduced mTORC1 activity are more tolerant to blockage of eIF4E-dependent translation, and their bivalent metabolism allows for translating selective mRNAs via both eIF4E-dependent and eIF4E-independent/eIF4A2-dependent pathways to form a more compact naïve proteome. Globally up-regulated proteostasis system and down-regulated post-translational modification system help to further refine and maintain the naïve proteome that is compatible with the more rapid cycling of naïve hESCs, where CDK1 plays an indispensable coordinative role.

2021-12-10 | PXD030230 | Pride

Reorganization of enhancer patterns in transition from naïve to primed pluripotency (ChIP-seq)

Project description:Naïve and primed pluripotency is characterized by distinct signaling requirements, transcriptomes and developmental properties, but both cellular states share key transcriptional regulators, Oct4, Sox2 and Nanog. Here we demonstrate that transition between these two pluripotent states is associated with widespread Oct4 relocalization, mirrored by global rearrangement of enhancer chromatin landscapes. Our genomic and biochemical analyses identified candidate mediators of primed state-specific Oct4 binding, including Otx2 and Zic2/3. Even in the absence of other differentiation cues, premature Otx2 overexpression is sufficient to exit the naïve state, induce transcription of a large subset of primed pluripotency-associated genes and redirect Oct4 to thousands of previously inaccessible sites. However, ability of Otx2 to engage new enhancer regions is determined by its levels, cis-encoded properties of the sites and signaling environment. Our results illuminate regulatory mechanisms underlying pluripotency and suggest that capacity of transcription factors such as Otx2 and Oct4 to function as pioneers is highly context-dependent ChIP-seq analysis was performed to map enhancers and associated transcription factors. We used H3K27ac, H3K4me1 and p300 to call enhancers from 2 different pluripotent cell states: ESC and EpiLC. In addition we performed ChIP-seq for Oct4 and Otx2 from these cell states. All these experiments were carried out in replicates, for the EpiLC state the replicates were performed with and without ActivinA. Additionally we carried out ChIPseq for Otx2 and Oct4 in Otx2ko cell lines in which we integrated an inducible Otx2 gene before and after induction with doxycycline.

2014-06-05 | E-GEOD-56098 | biostudies-arrayexpress

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