Oct4 differentially regulates chromatin opening and enhancer transcription in pluripotent stem cells
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ABSTRACT:
PROVIDER: PRJNA731505 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR14607351_1.fastq.gz | Fastqsanger.gz | |||
| SRR14607351_2.fastq.gz | Fastqsanger.gz | |||
| SRR14607352_1.fastq.gz | Fastqsanger.gz | |||
| SRR14607352_2.fastq.gz | Fastqsanger.gz | |||
| SRR14607353_1.fastq.gz | Fastqsanger.gz |
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Project description:The transcription factor Oct4 is essential for the maintenance and induction of stem cell pluripotency, but its functional roles are not fully understood. Here, we investigate the functions of Oct4 by depleting and subsequently recovering it in mouse embryonic stem cells and conducting a time-resolved multiomics analysis. Oct4 depletion leads to an immediate loss of its binding to enhancers, accompanied by a decrease in mRNA synthesis from its target genes that are part of the transcriptional network that maintains pluripotency. Gradual decrease of Oct4 binding to enhancers does not immediately change the chromatin accessibility but reduces transcription of enhancers. Conversely, partial recovery of Oct4 expression results in a rapid increase in chromatin accessibility, whereas enhancer transcription does not fully recover. These results indicate different concentration-dependent activities of Oct4. Whereas normal ESC levels of Oct4 are required for transcription of pluripotency enhancers, low levels of Oct4 are sufficient to retain chromatin accessibility, likely together with other factors such as Sox2.
2021-06-30 | GSE174774 | GEO
Project description:The transcription factor Oct4 is essential for the maintenance and induction of stem cell pluripotency, but its functional roles are not fully understood. Here, we investigate the functions of Oct4 by depleting and subsequently recovering it in mouse embryonic stem cells (ESCs) and conducting a time-resolved multiomics analysis. Oct4 depletion leads to an immediate loss of its binding to enhancers, accompanied by a decrease in mRNA synthesis from its target genes that are part of the transcriptional network that maintains pluripotency. Gradual decrease of Oct4 binding to enhancers does not immediately change the chromatin accessibility but reduces transcription of enhancers. Conversely, partial recovery of Oct4 expression results in a rapid increase in chromatin accessibility, whereas enhancer transcription does not fully recover. These results indicate different concentration-dependent activities of Oct4. Whereas normal ESC levels of Oct4 are required for transcription of pluripotency enhancers, low levels of Oct4 are sufficient to retain chromatin accessibility, likely together with other factors such as Sox2.
| S-EPMC9142147 | biostudies-literature
Project description:Naive and primed pluripotent human embryonic stem cells bear transcriptional similarity to pre- and post-implantation epiblast and thus constitute a developmental model for understanding the pluripotent stages in human embryo development. To identify new transcription factors that differentially regulate the unique pluripotent stages, we mapped open chromatin using ATAC-seq and found enrichment of the activator protein-2 (AP2) transcription factor binding motif at naive-specific open chromatin. We determined that the AP2 family member TFAP2C is upregulated during primed to naive reversion and becomes widespread at naive-specific enhancers. TFAP2C functions to maintain pluripotency and repress neuroectodermal differentiation during the transition from primed to naive by facilitating the opening of enhancers proximal to pluripotency factors. Additionally, we identify a previously undiscovered naive-specific POU5F1 (OCT4) enhancer enriched for TFAP2C binding. Taken together, TFAP2C establishes and maintains naive human pluripotency and regulates OCT4 expression by mechanisms that are distinct from mouse.
2018-04-25 | GSE101074 | GEO
Project description:To identify regulators of exit from the naïve pluripotent state we performed an enhancer trap screen under sensitized conditions. Briefly, haploid mouse ESCs with a Puromycin resistance gene under the control of Oct4 regulatory elements were mutagenized using viruses harboring enhancer trap constructs and subjected to differentiation in the presence of 3uM CHIR with concomitant selection for Oct4 expression. Selected cells were harvested after 16, 20, and 23 days and the extracted genomic DNA, together with genomic DNA of cells taken before selection, subjected to inverse PCR and sequencing. This allowed for mapping of enhancer trap integration sites and identifying genes whose targeting is enriched during selection.
2021-07-07 | E-MTAB-9796 | biostudies-arrayexpress
Project description:Nuclear architecture underlies the transcriptional programs within the cell to establish cell identity. As previously demonstrated, long-range chromatin interactions of the Oct4 distal enhancer (DE) are correlated with active transcription in naïve state embryonic stem cells. Here, we identify and characterize extreme long range interactions of the Oct4 DE through a novel CRISPR labeling technique we developed and chromosome conformation capture to identify lethal giant larvae 2 (Llgl2) and growth factor receptor-bound protein 7 (Grb7) as putative functional interacting target genes in different chromosomes. We show that the Oct4 DE directly regulates expression of Llgl2 and Grb7 in addition to Oct4. Expression of Llgl2 and Grb7 closely correlates with the pluripotent state, where knock down of either result in loss of pluripotency, and overexpression enhances somatic cell reprogramming. We demonstrated that biologically important interactions of the Oct4 DE can occur at extreme distances that are necessary for the maintenance of the pluripotent state.
2019-11-30 | GSE122753 | GEO
Project description:Nuclear architecture underlies the transcriptional programs within the cell to establish cell identity. As previously demonstrated, long-range chromatin interactions of the Oct4 distal enhancer (DE) are correlated with active transcription in naïve state embryonic stem cells. Here, we identify and characterize extreme long range interactions of the Oct4 DE through a novel CRISPR labeling technique we developed and chromosome conformation capture to identify lethal giant larvae 2 (Llgl2) and growth factor receptor-bound protein 7 (Grb7) as putative functional interacting target genes in different chromosomes. We show that the Oct4 DE directly regulates expression of Llgl2 and Grb7 in addition to Oct4. Expression of Llgl2 and Grb7 closely correlates with the pluripotent state, where knock down of either result in loss of pluripotency, and overexpression enhances somatic cell reprogramming. We demonstrated that biologically important interactions of the Oct4 DE can occur at extreme distances that are necessary for the maintenance of the pluripotent state.
2019-11-30 | GSE122748 | GEO
Project description:Naïve and primed pluripotent stem cells (PSCs) and germ cells express the Pou5f1 (Oct4) gene. The Oct4 gene contains two cis-regulatory elements, the distal (DE) and proximal enhancer (PE), which differentially control Oct4 expression in a cell-type- and stage-specific manner. Here, we generated double transgenic mice carrying both Oct4-ΔPE-GFP and Oct4-ΔDE-tdTomato (RFP), enabling us to simultaneously monitor the activity of DE and PE. Oct4 expression is stage-specifically regulated by DE and PE during embryonic and germ cell development. Using this dual reporter system, we successfully cultured pure populations of naïve (GFP+RFP-) and primed (GFP-RFP+) PSCs. We found that GFP+RFP- cells were metastable in serum-containing medium; stable naïve pluripotent cells were observed in medium containing two inhibitors (Meki and GSKi) but lacking serum. Finally, we suggest that the activity of Oct4 DE and PE is regulated by the repressive histone marks H3K9me3 and DNA methylation.
2015-03-19 | GSE67031 | GEO
Project description:The success of Yamanaka factor reprogramming mouse embryonic fibroblasts (MEFs) into induced pluripotent stem cells (iPSCs) suggests that some factor(s) must remodel the nuclei from a condensed state to a relaxed state to facilitate factor binding to target genes. We asked how the Yamanaka factor-dependent chromatin opening occurs. We found Oct4, but neither Sox2 nor Klf4, is responsible for the loosening of the condensed state. Oct4 acts as a pioneer factor that facilitates the binding of Klf4 and the expression of epithelial genes in the early stage of reprogramming.
2021-03-09 | GSE129728 | GEO
Project description:Analysis of Oct4(Pou5f1)-dependent gene expression levels in mouse embryonic stem cells (ESCs). In order to robustly assess changes in gene expression levels orchestrated by the transcription factor Oct4, we used microarrays to profile the transcriptional activity of four ESC lines: Two of these cell lines have been genetically engineered to express Oct4 at reduced levels (Oct+/-: OKO160 and ZHTc6), while the other two were expressing Oct4 at wild-type levels (Oct4+/+: E14Tg2a and OctGIP). Genes that showed significant and consistent changes between the Oct4-states were considered putative transcriptional targets of Oct4.
2013-05-03 | E-MTAB-1619 | biostudies-arrayexpress
Project description:Forced expression of four transcription factors Oct4,Sox2, Klf4 and Myc (OSKM) induces somatic cell reprogramming towards pluripotency. Major efforts have been made to characterize the molecular events involved in this process. Yet, it remains elusive how gene expression change, epigenetic landscape remodelling and cell fate conversion are triggered by expression of these Yamanaka factors.To address this gap,we utilized a secondary inducible reprogramming system and performed genome-wide profilings of Oct4 binding, histone modification(H3K4me3/H3K27me3/H3K4me1/H3K27ac), and gene expression analysis during this process. Through integrative analysis, we revealed stage-specific Oct4 binding and enhancer signatures in consistence with gene expression changes,in which the initial regression of somatic program is followed by the gradual acquisition of pluripotent program. Oct4 preferatially binds to H3K4me1 marked enhancer regions and Oct4 binding is positively correlated with active mark H3K27ac. Moreover,we observed significant enhancer activation of epigenetic related genes, especially acetylation associated genes, prior to pluripotency network activation, suggesting a pivotal role of epigenetic remodelling in the process of pluripotency acquisition and maintenance. We used ChIP-seq to explore the global changes of Oct4 binding profiling during OSKM-mediated somatic cell reprogramming. The exogenous Oct4 was tagged with 3XFlag, thus we used anti-flag antibody to monitor exogenous Oct4 changes; anti-Oct4 antibody which recognizes both endogenous and exogenous Oct4 was used to monitor total Oct4 changes during iPSC induction. In addition, we also examined genome-wide H3K4me1/H3K27ac/H3K4me3/H3K27me3/RNAPII profiling during 3Flag-OSKM 2' reprogramming.
2015-12-31 | E-GEOD-67520 | biostudies-arrayexpress