PRC2 Promotes Canalisation During Endodermal Differentiation [4sU-seq]
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1208097 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR31933724_1.fastq.gz | Fastqsanger.gz | |||
| SRR31933724_2.fastq.gz | Fastqsanger.gz | |||
| SRR31933725_1.fastq.gz | Fastqsanger.gz | |||
| SRR31933725_2.fastq.gz | Fastqsanger.gz | |||
| SRR31933726_1.fastq.gz | Fastqsanger.gz |
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Project description:PRC2 Promotes Canalisation During Endodermal Differentiation
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Project description:PRC2 Promotes Canalisation During Endodermal Differentiation [ChIP-Seq]
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Project description:In this study we employed a mouse embryonic stem cell (ESCs) differentiation system to convert pluripotent ESCs into Anterior Definitive Endoderm (ADE) to model primitive streak formation and early gastrulation. To monitor the progression of the differentiation we utilised a dual reporter mESC line (B6) bearing fluorescent reporters knocked in to the Gsc (marker of the PS/mesendoderm tagged with GFP) and Hhex (marker of definitive endoderm lineages tagged with Redstar) loci. To establish the transcriptional changes which occurred during a phase of differentiation that resembles the epithelial to mesenchymal transition (EMT) at the primitive streak (PS), we performed 4sU-seq analysis on FACS sorted GSC negative and positive populations from day 3 and day 4 of differentiation. Using this approach, in combination with genome-wide gene expression analysis and ChIP-seq data, we: i). Found that changes in the gene expression where primarily regulated at the levels of transcription; ii). Identified putative enhancer elements with bi-directional transcription signatures proximal to developmentally regulated genes; iii). Determined that transcriptional upregulation of genes did not require the prior loss of H3K27me3 at gene TSSs.
2025-01-13 | GSE286193 | GEO
Project description:In this study we employed a mouse embryonic stem cell in vitro system to differentiate ESCs into Anterior Definitive Endoderm (ADE) to model primitive streak formation and early gastrulation. To establish the gene expression changes which occurred during this differentiation we performed whole genome expression analysis on RNA isolated from FACS purified cell populations. We utilised a dual reporter mESC line (B6), bearing fluorescent reporters knocked in to the Gsc (GFP) and Hhex (Redstar) loci. GSC is a marker of the PS/mesendoderm and HHEX marks definitive endoderm lineages and expression of these reporters allowed us to isolate developmentally distinct populations during the differentiation. Using the expression profile of the untreated differentiation as a reference, we investigated the developmental impact of impaired H3K27me3 deposition on ADE differentiation by inhibiting EZH2, the core catalytic component of polycomb repressive complex 2 (PRC2) using the small molecule inhibitor EPZ6438. We found that ADE differentiation recapitulated the in vivo developmental tradjectory and that PRC2 inhibition enhanced endodermal differentiation efficiency, but did so at the cost of lineage fidelity.
2025-01-13 | GSE286087 | GEO
Project description:The genetic circuitry that encodes the developmental programme of mammals is regulated by transcription factors and chromatin modifiers. During early gestation, the three embryonic germ layers are established in a process termed gastrulation. The impact of deleterious mutations in chromatin modifiers such as the polycomb proteins manifests during gastrulation, leading to early developmental failure and lethality in mouse models. Embryonic stem cells have provided key insights into the molecular function of polycomb proteins, but it is impossible to fully appreciate the role of these epigenetic factors in development, or how development is perturbed due to their deficiency, in the steady-state. To address this, we have employed a tractable embryonic stem cell differentiation system to model primitive streak formation and early gastrulation. Using this approach, we find that loss of the repressive polycomb mark H3K27me3 is delayed relative to transcriptional activation, indicating a subordinate rather than instructive role in gene repression. Despite this, chemical inhibition of polycomb enhanced endodermal differentiation efficiency, but did so at the cost of lineage fidelity. These findings highlight the importance of the polycomb system in stabilising the developmental transcriptional response and, in so doing, in shoring up cellular specification.
| S-EPMC11813121 | biostudies-literature
Project description:ChIP-seq was performed to determine the transcriptional activity of genes during endodermal differentiation RNA pol II occupancy and histone marks of elongation and gene repression were analyzed during early endodermal differentiation
2012-09-25 | E-GEOD-41111 | biostudies-arrayexpress
Project description:ChIP-seq was performed to determine the transcriptional activity of genes during endodermal differentiation
2012-09-25 | GSE41111 | GEO
Project description:In this study we employed a mouse embryonic stem cell (ESCs) differentiation system to convert pluripotent ESCs into Anterior Definitive Endoderm (ADE) to model primitive streak formation and early gastrulation. To monitor the progression of the differentiation we utilised a dual reporter mESC line (B6) bearing fluorescent reporters knocked in to the Gsc (marker of the PS/mesendoderm tagged with GFP) and Hhex (marker of definitive endoderm lineages tagged with Redstar) loci. To monitor changes in the chromatin landscape during this differentiation we performed ChIP-seq for H3K27me3 and H3K4me3 (modifications associated with gene repression and activation respectively) in each of nine FACs sorted ADE populations. Using this approach, in combination with genome-wide gene expression analysis, we; i). Found that changes in gene expression/transcription were both predictive of and predicted by dynamic changes in the levels of these histone modifications at gene promoters; ii). Found that changes in H3K27me3 levels at TSS are more dynamic than the levels of H3K4me3; iii). Determined that transcriptional upregulation of genes did not require the prior loss of H3K27me3 at gene TSSs.
2025-01-13 | GSE286192 | GEO
Project description:Post-translational modifications of proteins are crucial to the regulation of their activity and function. As a newly discovered acylation modification, crotonylation of non-histone proteins remains largely unexplored, particularly in human embryonic stem cells (hESCs). Here we report the investigation of induced crotonylation in hESCs, which resulted in hESCs of different pluripotency states differentiating into the endodermal lineage. We showed that increased protein crotonylation in hESCs was accompanied by transcriptomic shifts and decreased glycolysis. Through large-scale profiling of non-histone protein crotonylation, we identified metabolic enzymes as major targets of inducible crotonylation in hESCs. We further discovered GAPDH as a key glycolytic enzyme regulated by crotonylation during endodermal differentiation from hESCs, where crotonylation of GAPDH decreased its enzymatic activity thereby leading to reduced glycolysis. Our study demonstrates that crotonylation of glycolytic enzymes may be crucial to metabolic switching and cell fate determination in hESCs.
2022-10-27 | PXD027007 | Pride