Discovery of Competent Chromatin Regions in Human Embryonic Stem Cells [scRNA-seq]
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE290596 | GEO | 2025/03/01
REPOSITORIES: GEO
Similar Datasets
Project description:It remains unclear how ESCs rapidly establish enhancer regulatory elements to activate lineage-specific genes at the earliest differentiation stages. Previous studies suggest that some tissue-specific enhancers are pre-marked in ESCs with permissive features that support their competence to induce gene expression in response to the binding of lineage transcription factors (TFs). However, the absence of functional assays to identify chromatin regions with the competence to activate gene expression upon TF binding has impeded to better define any pre-marking features and their role on the transcriptional competence of the chromatin. To address this, we leveraged a CRISPR-activation(a) system to systematically interrogate the presence of chromatin regions able to induce the expression of 5 lineage-specific genes that are inactive in human ESCs (hESCs). Multiple CRISPRa screens discovered 42 regions, which we termed Competent Chromatin Regions (CCRs), that can induce the expression of the 5 lineage genes upon CRISPRa targeting. ChIP seq analyses showed that CCRs do not represent primed or active enhancers, since they are not enriched in H3K4me1 or H3K27ac histone modifications. Instead, CCRs are characterized by the enriched occupancy of OCT4, NANOG and demethylation factors TET1 and QSER1, which prevent DNA hypermethylation. Although CCRs are exclusively found at the topologically associated domains shared with their related genes, we found they do not require an enrichment in pre-established chromatin contacts to exert their function. To assess the extent of our findings, we simulated the earliest stages of lineage differentiation by inducing the expression of the lineage TF FOXA2 in undifferentiated hESCs and we found it preferentially binds to the regions predicted as CCRs. Our results suggest that the factors enriched at CCRs facilitate the binding of lineage TFs and enable ESCs to promptly activate the expression of lineage genes. This study advances our understanding of pluripotency regulation in ESCs by identifying a novel type of regulatory regions that supports their developmental plasticity.
2023-06-01 | GSE233635 | GEO
Project description:It remains unclear how ESCs rapidly establish enhancer regulatory elements to activate lineage-specific genes at the earliest differentiation stages. Previous studies suggest that some tissue-specific enhancers are pre-marked in ESCs with permissive features that support their competence to induce gene expression in response to the binding of lineage transcription factors (TFs). However, the absence of functional assays to identify chromatin regions with the competence to activate gene expression upon TF binding has impeded to better define any pre-marking features and their role on the transcriptional competence of the chromatin. To address this, we leveraged a CRISPR-activation(a) system to systematically interrogate the presence of chromatin regions able to induce the expression of 5 lineage-specific genes that are inactive in human ESCs (hESCs). Multiple CRISPRa screens discovered 42 regions, which we termed Competent Chromatin Regions (CCRs), that can induce the expression of the 5 lineage genes upon CRISPRa targeting. ChIP seq analyses showed that CCRs do not represent primed or active enhancers, since they are not enriched in H3K4me1 or H3K27ac histone modifications. Instead, CCRs exhibit a significant enrichment in POU sequence motifs, along with higher levels of binding by OCT4 and other pluripotent TFs. CCRs have an enriched presence of several repressive and activating chromatin-associated factors, including the DNA demethylation factors TET1 and QSER1 and various HDAC enzymes, which regulate their transcriptional competence. Although CCRs are exclusively found at the topologically associated domains shared with their related genes, we found they do not require an enrichment in pre-established chromatin contacts to exert their function. To assess the extent of our findings, we simulated the earliest stages of lineage differentiation by inducing the expression of the lineage TF FOXA2 in undifferentiated hESCs and we found it preferentially binds to the regions predicted as CCRs. Our results suggest that the factors enriched at CCRs facilitate the binding of lineage TFs and enable ESCs to promptly activate the expression of lineage genes. This study advances our understanding of pluripotency regulation in ESCs by identifying a novel type of regulatory regions that supports their developmental plasticity.
2023-06-01 | GSE233636 | GEO
Project description:It remains unclear how ESCs rapidly establish enhancer regulatory elements to activate lineage-specific genes at the earliest differentiation stages. Previous studies suggest that some tissue-specific enhancers are pre-marked in ESCs with permissive features that support their competence to induce gene expression in response to the binding of lineage transcription factors (TFs). However, the absence of functional assays to identify chromatin regions with the competence to activate gene expression upon TF binding has impeded to better define any pre-marking features and their role on the transcriptional competence of the chromatin. To address this, we leveraged a CRISPR-activation(a) system to systematically interrogate the presence of chromatin regions able to induce the expression of 5 lineage-specific genes that are inactive in human ESCs (hESCs). Multiple CRISPRa screens discovered 42 regions, which we termed Competent Chromatin Regions (CCRs), that can induce the expression of the 5 lineage genes upon CRISPRa targeting. ChIP seq analyses showed that CCRs do not represent primed or active enhancers, since they are not enriched in H3K4me1 or H3K27ac histone modifications. Instead, CCRs exhibit a significant enrichment in POU sequence motifs, along with higher levels of binding by OCT4 and other pluripotent TFs. CCRs have an enriched presence of several repressive and activating chromatin-associated factors, including the DNA demethylation factors TET1 and QSER1 and various HDAC enzymes, which regulate their transcriptional competence. Although CCRs are exclusively found at the topologically associated domains shared with their related genes, we found they do not require an enrichment in pre-established chromatin contacts to exert their function. To assess the extent of our findings, we simulated the earliest stages of lineage differentiation by inducing the expression of the lineage TF FOXA2 in undifferentiated hESCs and we found it preferentially binds to the regions predicted as CCRs. Our results suggest that the factors enriched at CCRs facilitate the binding of lineage TFs and enable ESCs to promptly activate the expression of lineage genes. This study advances our understanding of pluripotency regulation in ESCs by identifying a novel type of regulatory regions that supports their developmental plasticity.
2023-06-01 | GSE233637 | GEO
Project description:Embryonic stem cells (ESCs) can be maintained in the naïve state through inhibition of Mek1/2 and Gsk3 (2i). A relevant effect of 2i is the inhibition of Cdk8/19, which are negative regulators of the Mediator complex, responsible for the activity of enhancers. Inhibition of Cdk8/19 (Cdk8/19i) stimulates enhancers and, similar to 2i, stabilizes ESCs in the naïve state. Here, we use mass spectrometry to describe the molecular events (phosphoproteome, proteome, and metabolome) triggered by 2i and Cdk8/19i on ESCs. Our data reveal widespread commonalities between these two treatments, suggesting overlapping processes. We find that post-transcriptional de-repression by both 2i and Cdk8/19i might support the mitochondrial capacity of naive cells. However, proteome reprogramming in each treatment is achieved by different mechanisms. Cdk8/19i acts directly on the transcriptional machinery, activating key identity genes to promote the naïve program. In contrast, 2i stabilizes the naïve circuitry through, in part, de-phosphorylation of downstream transcriptional effectors.
2021-02-10 | MTBLS301 | MetaboLights
Project description:RUNX1B expression distinguishes megakaryocytic and erythroid lineage fate in adult hematopoiesis
2019-05-14 | E-GEOD-68958 | ExpressionAtlas
Project description:ZNF462 haploinsufficiency is linked to Weiss-Kruszka Syndrome, a genetic disorder characterized by neurodevelopmental defects including Autism. Though conserved in vertebrates and essential for embryonic development the molecular functions of ZNF462 remain unclear. We identified its murine homolog ZFP462 in a screen for mediators of epigenetic gene silencing. Here, we show that ZFP462 safeguards neural lineage specification of mouse embryonic stem cells (ESCs) by targeting the H3K9-specific histone methyltransferase complex G9A/GLP to silence mesoendodermal genes. ZFP462 binds to transposable elements (TEs) that are potential enhancers harboring ESC-specific transcription factor (TF) binding sites. Recruiting G9A/GLP, ZFP462 seeds heterochromatin, restricting TF binding. Loss of ZFP462 in ESCs results in increased chromatin accessibility at target sites and ectopic expression of mesoendodermal genes. Taken together, ZFP462 confers lineage- and locus-specificity to the broadly expressed epigenetic regulator G9A/GLP. Our results suggest that aberrant activation of lineage non-specific genes in the neuronal lineage underlies ZNF462-associated neurodevelopmental pathology.
2023-05-10 | PXD037238 | Pride
Project description:The Nucleosome Remodeling and Deacetylase (NuRD) complex plays an important role in gene expression regulation, stem cell self-renewal, and lineage commitment. Yet little is known about the dynamics of NuRD during cellular differentiation. Here, we study these dynamics using genome-wide profiling and quantitative interaction proteomics in mouse embryonic stem cells (ESCs) and neural progenitor cells (NPCs). The genomic targets of NuRD are highly dynamic during differentiation, with most binding occurring at cell-type specific promoters and enhancers. We identify ZFP296 as a novel, ESC-specific NuRD interactor that also interacts with the SIN3A complex. ChIP-sequencing in Zfp296 knockout (KO) ESCs reveals decreased NuRD binding both genome-wide and at ZFP296 binding sites, although this has little effect on the transcriptome. Nevertheless, Zfp296 KO ESCs exhibit delayed induction of lineage-specific markers upon differentiation to embryoid bodies. In summary, we identify an ESC-specific NuRD interacting protein which regulates genome-wide NuRD binding and cellular differentiation.
2018-10-11 | PXD010512 | Pride
Project description:RNA Sequencing of H1 WT hESCs, H1 QSER1 KO hESCs, H1 TET1 KO hESCs, H1 QSER1/TET1 DKO hESCs, WT Day10 embryoid bodies (EBs), QSER1 KO Day10 EBs, TET1 KO Day10 EBs, QSER1/TET1 DKO Day10 EBs, WT pancreatic progenitors (PP1), QSER1 KO PP1, TET1 KO PP1, and QSER1/TET1 DKO PP1. DNA methylation is essential to mammalian development, and dysregulation can cause serious pathological conditions. Key enzymes responsible for deposition and removal of DNA methylation are known, but how they cooperate to tightly regulate the methylation landscape remains a central question. Utilizing a knockin DNA methylation reporter, we performed a genome-wide CRISPR/Cas screen in human embryonic stem cells to discover DNA methylation regulators. The top screen hit was an uncharacterized gene QSER1, which proved to be a key guardian of bivalent promoters and poised enhancers of developmental genes, especially those residing in DNA methylation valleys (or canyons). We further demonstrate cooperation of QSER1 and TET1 through genetic and biochemical interactions to inhibit DNMT3-mediated de novo methylation and safeguard developmental programs.
2021-03-19 | GSE169209 | GEO
Project description:We analyzed the genome-wide binding of Sox2 and POU factor partner factors, Oct4 in ESCs (using published datasets PMID:18692474 and GSM307137, GSM307154, GSM307155) and Brn2 in NPCs. We found that Sox2 and Oct4 co-occupied a large subset of promoters and enhancers in ESCs, but that Sox2 and Brn2 co-occupy predominantly enhancers. Further, we overexpressed Brn2 in differentiating ESCs and showed that ectopic Brn2 recruited Sox2 to NPC-specific targets, resulting in skewed differentiation towards the neural lineage. Examination of transcription factor binding in ESCs, NPCs, and differentiating ESCs by ChIP-Seq.
2013-02-20 | E-GEOD-35496 | biostudies-arrayexpress
Project description:Conventional rabbit embryonic stem cell (ESC) lines are derived from the inner cell mass (ICM) of pre-implantation embryos using methods and culture conditions established for primate ESCs (partial dissociation with collagenase and culture with FGF2). In the present work, we explored the capacity of rabbit ICM to give rise to ESC lines using conditions similar to those utilized to generate ESCs in mice.
2017-02-12 | GSE79195 | GEO