DNA (de)methylation in embryonic stem cells controls CTCF-dependent chromatin boundaries
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ABSTRACT:
PROVIDER: PRJNA471879 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR7179720_1.fastq.gz | Fastqsanger.gz | |||
| SRR7179720_2.fastq.gz | Fastqsanger.gz | |||
| SRR7179730.fastq.gz | Fastqsanger.gz | |||
| SRR7179721_1.fastq.gz | Fastqsanger.gz | |||
| SRR7179721_2.fastq.gz | Fastqsanger.gz |
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Project description:DNA (de)methylation in embryonic stem cells controls CTCF-dependent chromatin boundaries
| PRJNA433816 | ENA
Project description:The interplay of DNA (de)methylation and the architectural chromatin protein CTCF is an important regulator of cellular differentiation, but molecular mechanisms determining differential CTCF binding are not well understood. Mouse embryonic stem cells (ESCs) contain up to 10% of CpG residues in 5-hydroxymethylated form (5hmC) and smaller amounts in 5-formylated or 5-carboxylated forms (5fC, 5caC). Here, we studied double knock out ESCs (DKO) deficient for TET1 and TET2 enzymes which are responsible for the conversion of 5mC to 5hmC, 5fC and 5caC. For both wild type (WT) and DKO cells, we measured changes in nucleosome positions, CTCF binding, DNA methylation and gene expression. Our integrative data analysis combined with biophysical modelling suggests that both differential (de)methylation and CTCF binding are to a large degree predictable from the DNA sequence. Common CTCF sites that remained bound in DKO cells were significantly enriched at unmethylated CpG islands, while CTCF loss was associated with differential DNA methylation. 5hmCs and 5fCs had the opposite effects in terms of CTCF priming: CTCF was preferentially lost from sites that were marked in WT cells by 5hmCs but not 5fCs. Interestingly, the losses of CTCF at TAD boundaries lead to aberrant spreading of DNA methylation, as well as downregulation of neighbouring genes. Overall, our study clarifies the fundamental mechanism of differential CTCF binding and provides evidence of DNA sequence-encoded temporal chromatin changes during cell differentiation.
2019-03-26 | GSE110460 | GEO
Project description:Coordinated changes of DNA (de)methylation, nucleosome positioning and chromatin binding of the architectural protein CTCF play an important role for establishing cell type specific chromatin states during differentiation. To elucidate molecular mechanisms that link these processes we studied the perturbed DNA modification landscape in mouse embryonic stem cells (ESCs) carrying a double knockout (DKO) of the Tet1 and Tet2 dioxygenases. These enzymes are responsible for the conversion of 5-methylcytosine (5mC) into its hydroxymethylated (5hmC), formylated (5fC) or carboxylated (5caC) forms. We determined changes in nucleosome positioning, CTCF binding, DNA methylation and gene expression in DKO ESCs, and developed biophysical models to predict differential CTCF binding. Methylation-sensitive nucleosome repositioning accounted for a significant portion of CTCF binding loss in DKO ESCs, while unmethylated and nucleosome-depleted CpG islands were enriched for CTCF sites that remained occupied. A number of CTCF sites also displayed direct correlations with the CpG modification state: CTCF was preferentially lost from sites that were marked with 5hmC in wild type cells but not from 5fC enriched sites. In addition, we found that some CTCF sites can act as bifurcation points defining the differential methylation landscape. CTCF loss from such sites, e.g. at promoters, boundaries of chromatin loops and topologically associated domains (TADs), was correlated with DNA methylation/demethylation spreading and can be linked to downregulation of neighbouring genes. Our results reveal a hierarchical interplay between cytosine modifications, nucleosome positions and DNA sequence that determines differential CTCF binding and regulates gene expression.
2019-03-25 | GSE114599 | GEO
Project description:Coordinated changes of DNA (de)methylation, nucleosome positioning, and chromatin binding of the architectural protein CTCF play an important role for establishing cell-type-specific chromatin states during differentiation. To elucidate molecular mechanisms that link these processes, we studied the perturbed DNA modification landscape in mouse embryonic stem cells (ESCs) carrying a double knockout (DKO) of the Tet1 and Tet2 dioxygenases. These enzymes are responsible for the conversion of 5-methylcytosine (5mC) into its hydroxymethylated (5hmC), formylated (5fC), or carboxylated (5caC) forms. We determined changes in nucleosome positioning, CTCF binding, DNA methylation, and gene expression in DKO ESCs and developed biophysical models to predict differential CTCF binding. Methylation-sensitive nucleosome repositioning accounted for a significant portion of CTCF binding loss in DKO ESCs, whereas unmethylated and nucleosome-depleted CpG islands were enriched for CTCF sites that remained occupied. A number of CTCF sites also displayed direct correlations with the CpG modification state: CTCF was preferentially lost from sites that were marked with 5hmC in wild-type (WT) cells but not from 5fC-enriched sites. In addition, we found that some CTCF sites can act as bifurcation points defining the differential methylation landscape. CTCF loss from such sites, for example, at promoters, boundaries of chromatin loops, and topologically associated domains (TADs), was correlated with DNA methylation/demethylation spreading and can be linked to down-regulation of neighboring genes. Our results reveal a hierarchical interplay between cytosine modifications, nucleosome positions, and DNA sequence that determines differential CTCF binding and regulates gene expression.
| S-EPMC6499307 | biostudies-literature
Project description:CCCTC-binding factor (CTCF) is a conserved protein able to block communication between regulatory elements and gene promoters in flies and mammals. Here, we studied CTCF function in the Drosophila central nervous system (CNS) in which we find CTCF plays a vital role. Hi-C experiments on dissected larval CNSs of wildtype controls and CTCF[0] mutants that completely lack CTCF revealed that CTCF forms hundreds of physical boundaries in fly chromosomes.
2021-01-18 | GSE146750 | GEO
Project description:An increasing number of genes involved in chromatin structure and epigenetic regulation has been implicated in a variety of developmental disorders, often including intellectual disability. By trio exome sequencing and subsequent mutational screening we now identified two de novo frameshift mutations and one de novo missense mutation in the CTCF gene in individuals with intellectual disability, microcephaly and growth retardation. Furthermore, a patient with a larger deletion including CTCF was identified. CTCF (CCCTC-binding factor) is one of the most important chromatin organizers in vertebrates and is involved in various chromatin regulation processes such as higher order of chromatin organization, enhancer function, and maintenance of three-dimensional chromatin structure. Transcriptome analyses in all three patients with point mutations revealed deregulation of genes involved in signal transduction and emphasized the role of CTCF in enhancer-driven expression of genes. Our findings indicate that haploinsufficiency of CTCF affects genomic interaction of enhancers and their regulated gene promoters that drive developmental processes and cognition. Comparison of lymphocyte gene expression between 3 de novo CTCF mutation patients and 8 controls (4 technical replicates each, no biological replicates).
2013-06-01 | E-GEOD-46831 | biostudies-arrayexpress
Project description:Interplay between CTCF boundaries and a super enhancer controls cohesin extrusion trajectories and gene expression
| PRJNA725234 | ENA
Project description:The genome is partitioned into Topologically Associating Domains (TADs). About half of the boundaries of these TADs exhibit transcriptional activity and are correlated with better TAD insulation. However, the association between these transcripts and TAD insulation, enhancer:promoter interactions and transcription of genes remains unknown. Here we investigate the functional roles of these bRNAs (boundary-RNA) in boundary insulation and consequent effects on enhancer-promoter interactions and TAD transcription genome-wide and more specifically on the disease relevant INK4a/ARF TAD. Using a series of CTCF site deletions and bRNA knockdown experiments at this TAD boundary, we show a direct association of CTCF with the bidirectional bRNAs where the loss of bRNA triggers the concomitant loss of: CTCF at the TAD boundary, its insulation, enhancer:promoter interactions and gene transcription within the targeted TAD. We used another series of enhancer deletions and CRISPRi on promoters within INK4a/ARF TAD to better understand the regulation and origins of bRNA itself. We observe that the enhancers interact with boundaries and positively regulate the bRNA transcription at TAD boundaries. In return, the bRNAs recruit/stabilize the CTCF even on weak motifs within these boundaries and supports CTCF binding in clusters, therefore enhancing TAD insulation. This favors the intra-TAD enhancer:promoter interactions and leads to robust gene transcription. Functionally, bRNAs are more stable than eRNAs and their knockdown exactly mimics the CTCF site deletion. Furthermore, transcribing boundaries exhibit high TAD transcription in TCGA tumour datasets. Together, these results show that active enhancers directly mediate better insulation of TADs by activating the transcription at TAD boundaries triggering CTCF clustering at the boundary which results in better insulation and favours robust intra-TAD enhancer:promoter interactions to activate the gene transcription.
2022-12-28 | GSE180659 | GEO
Project description:CTCF plays an important role in 3D genome organization by adjusting insulation at TAD boundaries, where clustered CBS (CTCF-binding site) elements are often arranged in tandem array with a complex divergent or convergent orientation. Here using cPcdh and HOXD loci as a paradigm, we look into the clustered CTCF TAD boundaries and find that, counterintuitively, outward-oriented CBS elements are crucial for inward enhancer-promoter interactions as well as for gene regulation. Specifically, by combinatorial deletions of a series of putative enhancer elements in vivo or CBS elements in vitro, in conjunction with chromosome conformation capture and RNA-seq analyses, we show that deletions of outward-oriented CBS elements weaken the strength of long-distance intraTAD promoter-enhancer interactions and enhancer activation of target genes. Our data highlight the crucial role of outward-oriented CBS elements within the clustered CTCF TAD boundaries and have interesting implications on the organization principles of clustered CTCF sites within TAD boundaries.
2023-10-31 | GSE211024 | GEO
Project description:CTCF plays an important role in 3D genome organization by adjusting insulation at TAD boundaries, where clustered CBS (CTCF-binding site) elements are often arranged in tandem array with a complex divergent or convergent orientation. Here using cPcdh and HOXD loci as a paradigm, we look into the clustered CTCF TAD boundaries and find that, counterintuitively, outward-oriented CBS elements are crucial for inward enhancer-promoter interactions as well as for gene regulation. Specifically, by combinatorial deletions of a series of putative enhancer elements in vivo or CBS elements in vitro, in conjunction with chromosome conformation capture and RNA-seq analyses, we show that deletions of outward-oriented CBS elements weaken the strength of long-distance intraTAD promoter-enhancer interactions and enhancer activation of target genes. Our data highlight the crucial role of outward-oriented CBS elements within the clustered CTCF TAD boundaries and have interesting implications on the organization principles of clustered CTCF sites within TAD boundaries.
2023-10-31 | GSE210815 | GEO