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Total RNA-Seq on control, Polycomb null and H3K27R mutant mESCs and EpiLCs

ABSTRACT: Total RNA-Seq on control, Polycomb null and H3K27R mutant mESCs and EpiLCs

PROVIDER: PRJNA675033 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR12999100.fastq.gz	Fastqsanger.gz
	SRR12999101.fastq.gz	Fastqsanger.gz
	SRR12999102.fastq.gz	Fastqsanger.gz
	SRR12999103.fastq.gz	Fastqsanger.gz
	SRR12999104.fastq.gz	Fastqsanger.gz

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Total RNA-Seq on control, Polycomb null and H3K27R mutant mESCs and EpiLCs

Project description:Here we report the results of total RNASeq derived transcriptomes from naïve pluripotent mouse embryonic stem cells (mESCs) and pre-gastrulation epilblast like cells (EpiLCs) derived from mESCs following a 48 hour treatment with activin, FGF and knockout serum replacement as described in Hayashi et al., Cell 2011 (PMID: 21820164). We observe a strong concordance between histone mutant (H3K27R) cell lines and Polycomb null (SUZ12 knockout) steady state mESCs, with the primary effect of mutation resulting in gene de-repression. H3K27me3 is found strongly correlated with gene repression while H3K27ac is found strongly correlative with gene expression. We also show the lack of requirement for H3K27ac for gene activation upon differentiation of promoter or enhancer mediated EpiLC gene markers, leading us to conclude that transcription occurs independently of the requirement of H3K27ac.

2021-12-06 | GSE160975 | GEO

Single-cell transcriptome profiling during the in vitro differentiation of mouse ESCs (mESCs) into epiblast-like cells (EpiLCs).

Project description:We performed single-cell RNA sequencing (RNA-seq) during the in vitro transition of mouse ESCs (mESCs) from a naïve pluripotent state into epiblast-like cells (EpiLCs), a primed pluripotent state. We derived pseudotime expression trajectories to investigate transcript dynamics of key metabolic regulators, with the aim to identify metabolic pathways that potentially impact on early embryonic cell state transitions.

2018-12-06 | GSE107761 | GEO

Genome-wide maps of histone PTMs and co-factors in pluripotent mouse embryonic stem cells (mESCs) and epiblast-like cells (EpiLCs)

Project description:We report here the genome wide mapping of histone PTMs and chromatin bound factors in pluripotent control and H3K27R base edited mouse embryonic stem cells (mESCs) and epiblast-like cells (EpiLCs) using ChIP-Seq technology. We have deposited results from chromatin immunoprecipitations done using antibodies against Rpb1 (Pol-II), Med1,H3.3, H3K27me1, H3K27me2, H3K27me3 and H3K27ac (rabbit and mouse monoclonal antibodies). We show the loss of all H3K27 from H3.1/2/3 results in loss of associated K27 methylation and acetylation as expected. In such cells, there are only modest changes to MED1 or RNA Pol-II binding or activity that correlate with transcriptional status, suggesting that H3K27ac is not required to initiate or maintain transcription of genes, while loss of H3K27me3 associates with derepression of Polycomb target genes.

2021-12-06 | GSE160974 | GEO

WT and Hira-null undifferentiated mESCs and day15 differentiated cardiomyocytes

Project description:Purpose: The goals of this study are to compare transcriptome profiling (RNA-seq) resulting from the knockout of Hira in undifferentiated mouse embryonic stem cells (mESCs) and in day 15 differentiated cardiomyocytes.Methods: RNA extraction was done in duplicate from WT and Hira-null mESCs at day0 and day15 using TRIzol reagent. RNAseq was done onIllumina Nextseq500 and processed by the ICH genomics facility, reads were aligned and normalised using BOWTIE and DEseq R2 package. Gene lists were filtered using adjusted p-value ≤ 0.05 and absolute fold change ≥ 2. Results:We identified 1680 transcripts changed in the absence of HIRA in day 15 differentiated cardiomyocytes. GO term cardiovascular system development was the most downregulated gene set(p-value ≤ 0.01 and FDR ≤0.1. Conclusion: this study analysis the role of HIRA in early cardiac mesoderm development usinf an invitro mESCs model.

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WT and Hira-null undifferentiated mESCs and day15 differentiated cardiomyocytes

Project description:WT and Hira-null undifferentiated mESCs and day15 differentiated cardiomyocytes

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Transcriptional profiling by array of Klf2 wild-type and Klf2-Null mESCs cultured under 2i

Project description:The self-renewing pluripotent state was first captured in mouse embryonic stem cells (mESCs) over two decades ago. The standard condition requires the presence of serum and LIF, which provide growth promoting signals for cell expansion. However, there are pro-differentiation signals which destabilize the undifferentiated state of mESCs. The dual inhibition (2i) of the pro-differentiation Mek/Erk and Gsk3/Tcf3 pathways in mESCs is sufficient to establish an enhanced pluripotent “ground state” which bears features resembling the pre-implantation mouse epiblast. Gsk3 inhibition alleviates the repression of Esrrb, a transcription factor that can substitute for Nanog function in mESCs. The molecular mechanism that is mediated by Mek inhibition is however not clear. In this study, we investigate the pathway through which Mek inhibition operates to maintain ground state pluripotency. We have found that in mESCs, Kruppel-like factor 2 (Klf2) is a protein target of the Mek/Erk pathway; and that Klf2 protein is phosphorylated by Erk2 and subsequently degraded through the proteosome. It is therefore by Mek-inhibition through PD0325901 or 2i that enables the stabilization and accumulation of Klf2 to sustain ground state pluripotency. Importantly, we found that Klf2-null mESCs, while viable under LIF/Serum conditions, cannot be maintained and eventually gradually die within a few passages. Our result thus demonstrates that Klf2 is an essential factor of ground state pluripotency. Collectively, our study defines the Mek/Klf2 axis that cooperates with the Gsk3/Esrrb pathway in mediating ground state pluripotency.

2014-06-04 | E-MTAB-2366 | biostudies-arrayexpress

Single-cell transcriptome profiling during the in vitro differentiation of mouse ESCs (mESCs) into epiblast-like cells (EpiLCs).

Project description:Single-cell transcriptome profiling during the in vitro differentiation of mouse ESCs (mESCs) into epiblast-like cells (EpiLCs).

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Mapping Promoter CpG Methylation in mESCs

Project description:DNA methylation and histone modifications influence gene activities in a variety of mammalian cells. We report here the large scale mapping of DNA methylation patterns at proximal promoter regions in mouse embryonic stem cells (mESCs). A majority of methylated genes represent cell differentiation-associated genes that are repressed in mESCs. In contrast, unmethylated genes include many housekeeping and pluripotency genes such as STAT3 and Oct4/Nanog/Sox2, which are essential for ESC self-renewal. By comparing methylation patterns to the binding domains of Oct4/Nanog, Polycomb proteins, and histone H3 lysine (K) 4/27 trimethylation on gene promoters, we found that promoter DNA methylation is frequently the only epigenetic marker associated with a subset of silenced genes in mESCs that do not possess H3 K4/K27 trimethylation marks and are free from the binding of Polycomb proteins and the Oct4/Nanog transcription factors. Gene expression profiling of demethylated mESCs showed that a majority of up-regulated genes, including a subset of X-linked genes and many development genes, represent a distinct population of genes that are neither targeted by Polycomb and Oct4/Nanog, nor carry H3 K4/K27 trimethylation marks. Our data suggest that promoter methylation patterns in mESCs represent a unique epigenetic program that complements other regulatory mechanisms to allow the expression of pluripotency genes, but represses a subset of genes that will only be activated in specific cell lineages upon cell differentiation. Keywords: DNA Methylation, methylated DNA immunoprecipitation

2008-01-28 | GSE9172 | GEO

The dynamic interactome of Polycomb family complexes during stem cell differentiation

Project description:While the core subunits of Polycomb group (PcG) complexes are well characterized, little is known about the dynamics of these protein complexes during cellular differentiation. We used quantitative interaction proteomics to study PcG proteins in mouse embryonic stem cells (mESCs) and neural progenitor cells (NPCs). We found the stoichiometry of PRC1 and PRC2 to be highly dynamic during neural differentiation.

2016-05-19 | PXD003758 | Pride

Allele-specific mRNA expression analysis in 129/CAST hybrid mESCs by single-cell full-length total RNA-sequencing

Project description:Cell-to-cell heterogeneity in gene expression can even be observed in the same type of cells, present in a similar environment. Transcriptional bursting is thought to be one of contributing factors to the heterogeneity, but it remains elusive how the kinetic properties of transcriptional bursting (e.g. burst size, burst frequency, and noise induced by transcriptional bursting) are regulated in mammalian cells. Here, by using single-cell, full-length total RNA-sequencing, we performed genome-wide analysis of transcriptional bursting in mouse embryonic stem cells (mESCs). We found that the kinetics of transcriptional bursting is gene-specific and is determined by a combination of promoter and gene body binding proteins, including polycomb repressive complex 2 and transcription elongation-related factors.

2020-06-04 | GSE132589 | GEO

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