Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

DNA methylation oscillations at CpG poor enhancers in primed embryonic stem cells [PBAT Bisfulfite-seq]

ABSTRACT: Mouse embryonic stem cells (ESCs) primed for differentiation display dynamic heterogeneity characterised by stochastic switching between transcriptional states, and recent advances have highlighted the heterogeneous and dynamic nature of DNA methylation in these. Using single cell sequencing we report global oscillations in ESC DNA methylation that affect particularly CpG poor regions including distal enhancers. These oscillations are dependent on DNA methylation turnover by Dnmt3 and Tet enzymes and influence the probability of transcriptional state switching. Our observations suggest that regulated DNA methylation heterogeneity may contribute to lineage priming in cells poised for differentiation.

ORGANISM(S): Mus musculus

PROVIDER: GSE75973 | GEO | 2018/06/26

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

DNA methylation oscillations at CpG poor enhancers in primed embryonic stem cells [amplicon-Seq]

Project description:Mouse embryonic stem cells (ESCs) primed for differentiation display dynamic heterogeneity characterised by stochastic switching between transcriptional states, and recent advances have highlighted the heterogeneous and dynamic nature of DNA methylation in these. Using single cell sequencing we report global oscillations in ESC DNA methylation that affect particularly CpG poor regions including distal enhancers. These oscillations are dependent on DNA methylation turnover by Dnmt3 and Tet enzymes and influence the probability of transcriptional state switching. Our observations suggest that regulated DNA methylation heterogeneity may contribute to lineage priming in cells poised for differentiation.

2018-06-26 | GSE116163 | GEO

DNA methylation oscillations at CpG poor enhancers in primed embryonic stem cells [scRNA-Seq, scBS-Seq]

2018-06-26 | GSE116165 | GEO

DNA methylation oscillations at CpG poor enhancers in primed embryonic stem cells [single cell Bisulfite-seq]

2018-06-26 | GSE75974 | GEO

Genome-scale DNA methylation oscillations in pluripotent cells

Project description:Genome-scale DNA methylation oscillations in pluripotent cells

| PRJNA305881 | ENA

DNA methylation oscillations at CpG poor enhancers in primed embryonic stem cells [amplicon-Seq]

Project description:DNA methylation oscillations at CpG poor enhancers in primed embryonic stem cells [amplicon-Seq]

| PRJNA477530 | ENA

DNA methylation oscillations at CpG poor enhancers in primed embryonic stem cells [scRNA-Seq, scBS-Seq]

Project description:DNA methylation oscillations at CpG poor enhancers in primed embryonic stem cells [scRNA-Seq, scBS-Seq]

| PRJNA477527 | ENA

Adaptor molecule of DNA methylation in IECs

Project description:We previously reported that gut microbiota induce de novo DNA methylation of the TLR4 gene in intestinal epithelial cells. Since DNA methyltransferase (DNMT) 3 mediates the transfer of methyl groups to any gene undergoing de novo methylation, the question of how gut microbiota induce the recruitment of DNMT3 to specific genes, including TLR4, remains to be addressed. In this study, we tried to identify an adaptor molecule that recruits DNMT3b to the TLR4 gene by comparing expression of DNMT3-interacting proteins between IEC lines with hypermethylated and hypomethylated TLR4 gene.

2023-03-11 | PXD035777 | Pride

SINEultaneous profiling of epigenetic heterogeneity and transcriptome in single cells [PBAT]

Project description:Global changes in DNA methylation are observed in several developmental and disease contexts, and single-cell analyses are beginning to reveal the heterogeneous regulation of these processes. However, these studies are limited by the poor alignment rates and high sequencing demands associated with single-cell analysis of DNA methylation. We present single-cell transposable element methylation sequencing (scTEM-seq) for cost-effective estimation of global DNA methylation levels. By targeting high-copy LINE-1 and SINE Alu elements, we achieve amplicon bisulphite sequencing with thousands of annotated loci covered in each scTEM-seq library. Parallel transcriptome analysis of the same single cell is also performed to link global DNA methylation heterogeneity with transcriptional consequences. We apply scTEM-seq to KG1a acute myeloid leukaemia (AML) cells, and primary cells from an AML patient. Treatment of KG1a cells with the hypomethylating agent, decitabine, induces global DNA methylation heterogeneity associated with altered expression of viral response pathways. We also compare global levels of DNA methylation to expression of transposable elements and find a predominance of negative correlations in both the KG1a and patient cells. Finally, we observe co-ordinated upregulation of many transposable elements in a sub-set of decitabine treated KG1a cells. These observations suggest that viral mimicry processes important for epigenetic therapy and tumour immunogenicity are variably active in AML cells. By linking global DNA methylation heterogeneity with transcriptional consequences, scTEM-seq will refine our understanding of epigenetic regulation in cancer and beyond.

2022-04-13 | GSE171028 | GEO

Dynamic Enhancer DNA Methylation as Basis for Transcriptional and Cellular Heterogeneity of ESCs [RNA-seq]

Project description:Variable levels of DNA methylation have been reported at tissue-specific differential methylation regions (DMRs) overlapping enhancers, including super-enhancers (SEs) associated with key cell identity genes, but the mechanisms responsible for this intriguing behavior are not well understood. We used allele-specific reporters at the endogenous Sox2 and miR290 super-enhancers (SE) in embryonic stem cells and found that the allelic DNA methylation state is dynamically switching, resulting in cell-to-cell heterogeneity. Dynamic DNA methylation is driven by the balance between DNA methyl-transferases and transcription factor binding on one side, and co-regulated with the Mediator complex recruitment and H3K27ac level changes at regulatory elements on the other side. DNA methylation at the Sox2 and the miR290 SEs is independently regulated and has distinct consequences on the cellular differentiation state. Dynamic allele-specific DNA methylation at the two SEs was also seen at different stages in preimplantation embryos, revealing that methylation heterogeneity occurs in vivo.

2019-06-15 | GSE132414 | GEO

Dynamic Enhancer DNA Methylation as Basis for Transcriptional and Cellular Heterogeneity of ESCs [BiSulfite-seq]

2019-06-15 | GSE132404 | GEO