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CTCF chromatin residence time controls 3D genome organization, gene expression and DNA methylation in pluripotent cells

ABSTRACT: CTCF chromatin residence time controls 3D genome organization, gene expression and DNA methylation in pluripotent cells

PROVIDER: PRJNA644799 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR12172614.fastq.gz	Fastqsanger.gz
	SRR12172615.fastq.gz	Fastqsanger.gz
	SRR12172616.fastq.gz	Fastqsanger.gz
	SRR12172617.fastq.gz	Fastqsanger.gz
	SRR12172618.fastq.gz	Fastqsanger.gz

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CTCF chromatin residence time controls 3D genome organization, gene expression and DNA methylation in pluripotent cells [Hi-C]

Project description:CTCF chromatin residence time controls 3D genome organization, gene expression and DNA methylation in pluripotent cells [Hi-C]

| PRJNA644596 | ENA

CTCF chromatin residence time controls 3D genome organization, gene expression and DNA methylation in pluripotent cells [ChIP-Seq, RNA-seq, Med-Seq]

Project description:CTCF chromatin residence time controls 3D genome organization, gene expression and DNA methylation in pluripotent cells [ChIP-Seq, RNA-seq, Med-Seq]

| PRJNA644803 | ENA

CTCF chromatin residence time controls 3D genome organization, gene expression and DNA methylation in pluripotent cells [Hi-C]

Project description:The eleven zinc finger (ZF) protein CTCF regulates topologically associating domain (TAD) formation and transcription through selective binding to thousands of genomic sites. We replaced endogenous CTCF in mouse embryonic stem (ES) cells with GFP-tagged wildtype or mutant proteins lacking individual ZFs. We examined the various ES cell lines using next generation sequencing methods (ChIP-Seq, RNA-Seq, MedSeq, HiC) in order to identify additional determinants of CTCF positioning and function.

2021-06-04 | GSE153948 | GEO

CTCF chromatin residence time controls 3D genome organization, gene expression and DNA methylation in pluripotent cells [ChIP-Seq, RNA-seq, Med-Seq]

2021-06-04 | GSE154008 | GEO

CTCF chromatin residence time controls 3D genome organization, gene expression and DNA methylation in pluripotent cells

Project description:This SuperSeries is composed of the SubSeries listed below.

2021-06-04 | GSE154009 | GEO

CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription

Project description:Spatial genome organization and its effect on transcription remains a fundamental biological question. We applied an advanced ChIA-PET strategy to comprehensively map higher-order chromosome folding and chromatin interactions mediated by CTCF and RNAPII with haplotype specificity and nucleotide resolution in different human cell lineages. We find that CTCF-mediated interaction anchors serve as structural foci for spatial organization of constitutive genes concordant with CTCF-motif orientation, whereas RNAPII interacts within these structures by selectively drawing cell-type-specific genes towards CTCF-foci and forming RNAPII foci for coordinated transcription. Furthermore, allelic-variants linked to disease susceptibility are found to impact chromatin topology and transcriptional regulation. Importantly, 3D-genome simulation suggested a model of chromatin folding around chromosomal axes, where CTCF involves in defining the interface between condensed and open compartments for structural regulation. Our new 3D-genome strategy thus provides novel insights to explore the topological mechanism of human variations and diseases.

2015-12-11 | GSE72816 | GEO

Cell type specificity of chromatin organization mediated by CTCF and cohesin

Project description:CTCF sites are abundant in the genomes of diverse species but their function is enigmatic. We used chromosome conformation capture to determine long-range interactions among CTCF/cohesin sites over 2 Mb on human chromosome 11 encompassing the β-globin locus and flanking olfactory receptor genes. Although CTCF occupies these sites in both erythroid K562 cells and fibroblast 293T cells, the long-range interaction frequencies among the sites are highly cell type specific, revealing a more densely clustered organization in the absence of globin gene activity. Both CTCF and cohesins are required for the cell-type-specific chromatin conformation. Furthermore, loss of the organizational loops in K562 cells through reduction of CTCF with shRNA results in acquisition of repressive histone marks in the globin locus and reduces globin gene expression, whereas silent flanking olfactory receptor genes are unaffected. These results support a genome-wide role for CTCF/cohesin sites through loop formation that both influences transcription and contributes to cell-type-specific chromatin organization and function. Comparison of CTCF binding in K562 and 293T cells using ChIP-chip. 3 replicates each cell type, ChIP and input DNA for each replicate.

2011-01-13 | E-GEOD-26507 | biostudies-arrayexpress

SRF is a new player in 3D genome organization and stem cell pluripotency

Project description:Serum response factor (SRF) is a transcription factor essential for cell proliferation, differentiation, and migration, and is required for primitive streak and mesoderm formation in the embryo. The canonical roles of SRF are mediated by a diverse set of context-dependent cofactors. Here we show that SRF physically interacts with CTCF and cohesin subunits at TAD boundaries and loop anchors. SRF reinforces the insulation of TADs and promotes the formation of long-range chromatin loops. In ES cells, SRF associates with Oct4, Sox2, and Nanog and contributes to the formation of 3D pluripotency hubs. Our findings reveal new roles of SRF in higher-order chromatin organization.

2024-10-14 | PXD049365 | Pride

Clustering of CpG islands constitutes an important determinant of the interphase chromosome 3D organization [ChIP-Seq]

Project description:Using 4C-Seq experimental procedure we have characterized, in cultured chicken lymphoid and erythroid cells, genome-wide patterns of spatial contacts of several CpG islands scattered along the chromosome 14. A clear tendency for interaction of CpG islands present within the same and different chromosomes has been observed. Accordingly, preferential spatial contacts between Sp1 binding motifs, and other GC-rich genomic elements including DNA sequence motifs capable to form G-quadruplexes were demonstrated. On the other hand, an anchor placed in gene/CpG islands-poor area was found to form spatial contacts with other gene/CpG islands-poor areas within chromosome 14 and other chromosomes. These results corroborate the two compartments model of interphase chromosome spatial organization and suggest that clustering of CpG islands harboring promoters and origins of DNA replication constitutes an important determinant of the 3D organization of eukaryotic genome in the cell nucleus. Using ChIP-Seq experimental procedure we have mapped genome-wide the CTCF deposition sites in chicken lymphoid and erythroid cells subjected to the 4C analysis. A good correlation between the density of these sites and the level of 4C signals was observed for the anchors located in CpG islands. It is thus possible that CTCF contributes to the clustering of CpG islands revealed in our experiments. Using ChIP-Seq experimental procedure we have mapped genome-wide the CTCF deposition sites in chicken lymphoid and erythroid cells subjected to the 4C analysis. CTCF deposition sites in chicken lymphoid and erythroid (induced and non-induced) cells.

2014-03-01 | E-GEOD-51846 | biostudies-arrayexpress

CTCF-mediated 3D chromatin predetermines the gene expression program in the male germline (RNA-Seq)

Project description:Spermatogenesis is a unidirectional differentiation process that generates haploid sperm, but how the gene expression program that directs this process is established is largely unknown. Here we determine the high-resolution 3D chromatin architecture of male germ cells during spermatogenesis and show that CTCF-mediated 3D chromatin predetermines the gene expression program required for spermatogenesis. In undifferentiated spermatogonia, CTCF-mediated chromatin interactions between meiosis-specific super-enhancers (SE) loci and target genes precede activation of meiosis-specific SEs on autosomes. These meiotic SE recruit the master transcription factor A-MYB in meiotic spermatocytes, which strengthens their 3D contacts and instructs a burst of meiotic gene expression. We also find that at the mitosis-to-meiosis transition, the germline-specific Polycomb protein SCML2 resolves chromatin loops that are specific to mitotic spermatogonia. Moreover, SCML2 and A-MYB establish the unique 3D chromatin organization of sex chromosomes during meiotic sex chromosome inactivation. We propose that CTCF-mediated 3D chromatin organization enforces epigenetic priming that directs unidirectional differentiation, thereby determining the cellular identity of the male germline.

2024-12-13 | GSE272432 | GEO

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