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CTCF binds to an average of about 55,000 DNA sites in 19 diverse cell types (12 normal and 7 immortal) and in total 77,811 distinct binding sites across all 19 cell types. [29] CTCF's ability to bind to multiple sequences through the usage of various combinations of its zinc fingers earned it the status of a “multivalent protein”. [5] More ...

4. CTCF and cohesin share DNA binding sites. An unanticipated observation was the co-localization of cohesin with many of the chromosomal binding sites of CTCF [38–42]. Cohesin has always been associated with DNA replication and sister chromatid cohesion during the S, G2 and M phase of the cell cycle . It is a protein complex that contains ...

CCCTC-binding factor (CTCF) is an 82-kDa protein with 11 zinc fingers. 1 It was first identified as a transcriptional repressor of the chicken c-myc gene, a regulatory gene that encodes the c-myc ...

CTCF (CCCTC-binding factor) is a highly conserved multifunctional DNA-binding protein with thousands of binding sites genome-wide. Our previous work suggested that differences in CTCF's binding site sequence may affect the regulation of CTCF recruitment and its function. To investigate this possibil …

The presence of CpGs in the DNA consensus sequence of the CTCF-binding site supports the notion that methylation of cytosine residues at carbon 5 of the base to form 5-methylcytosine (5mC) in CpG ...

The CCCTC-binding factor (CTCF) is pivotal in orchestrating diverse biological functions across the human genome, yet the mechanisms driving its cell type-active DNA binding affinity remain ...

Specifically, CTCF-binding sites were found to be significantly overrepresented both on Hi-C fragments that had a large number of long-range interactions and at the boundaries of the topological domains that spatially organize the genome . In parallel with this changing understanding of the importance of CTCF, there has been remarkable growth ...

A CTCF-binding site (INSUL_MAN0004) webpage displays the flanking gene expression profiles and links to tracks of SNPs, genomic context and orthologous regions. Mammalian orthologous region track. Comparative genomic studies on human, mouse and rat may provide insights into the evolution of CTCF-binding sites. To this end, we created a track of ...

Given the differences in genome assemblies, we defined CTCF binding sites directly for each assembly, including the Telomere to Telomere (T2T) human genome assembly (Nurk et al., 2022) and the GRCm39/mm39 mouse genome assembly. We demonstrate that coordinate conversion (liftOver) is a viable way to obtain assembly-specific CTCF binding sites.

Summary: CTCF (CCCTC-binding factor) is an 11-zinc-finger DNA binding protein which regulates much of the eukaryotic genome's 3D structure and function. The diversity of CTCF binding motifs has led to a fragmented landscape of CTCF binding data. We collected position weight matrices of CTCF binding motifs and defined strand-oriented CTCF binding sites in the human and mouse genomes, including ...

Yet, or perhaps therefore, CTCF's exact function at a given genomic site is unpredictable. It appears to be determined by the associated transcription factors, by the location of the binding site relative to the transcriptional start site of a gene, and by the site's engagement in chromatin loops with other CTCF-binding sites, enhancers or gene ...

While CTCF binding sites are generally correlated with genes along the entire length of chromosomes, there are isolated regions that deviate from this trend . Two notable types of loci can be defined: one type of loci is characterized by a relative depletion of CTCF binding sites and the other by an enrichment of CTCF binding sites. We can ...

CTCF plays an important role in 3D genome organization by adjusting the strength of chromatin insulation at TAD boundaries, where clustered CBS (CTCF-binding site) elements are often arranged in a ...

CTCF has it all. The transcription factor binds to tens of thousands of genomic sites, some tissue-specific, others ultra-conserved. It can act as a transcriptional activator, repressor and insulator, and it can pause transcription. CTCF binds at ...

a CTCF ChIP-qPCR assaying all CTCF-binding sites at KLK locus was performed on control and CRISPR cells and demonstrates reduction of CTCF binding at CRISPR sites but retained binding at all other ...

Third, loss of site-specific CTCF binding was directly demonstrated using CUT&RUN. Histone modifications and histone variants are maintained in mitosis, suggesting a role in bookmarking of active CTCF sites. Finally, live-cell imaging, fluorescence recovery after photobleaching, and single molecule tracking showed that almost all CTCF chromatin ...

DconnLoop demonstrated higher peak enrichment near CTCF binding sites, suggesting greater reliability in chromatin loop detection. A key protein involved in the formation of chromatin loops is the CCCTC-binding factor (CTCF), a highly conserved zinc-finger DNA-binding protein. CTCF recognizes and binds to specific DNA sequences, with a ...

CTCF binding sites are associated with different genetic elements. The majority of sites are intergenic and co-localize with cohesin. In addition, a fraction of CTCF binding sites are located near RNA polymerase III (RNAPIII) type II genes (e.g. tRNA and SINE elements) and ETC loci, suggesting that TFIIIC and CTCF may cooperate in some aspects of the function of this protein.

The CTCF binding sites at the TAD boundaries are usually represented by clusters, which probably ensure CTCF binding to the genomic targets for a longer time . According to the loop extrusion model, the cohesin complexes are only transiently blocked at a certain CTCF site and can continue to pull chromatin after crossing the block created by ...

Background: CTCF (CCCTC-binding factor) is an evolutionarily conserved zinc finger protein involved in diverse functions ranging from negative regulation of MYC, to chromatin insulation of the beta-globin gene cluster, to imprinting of the Igf2 locus. The 11 zinc fingers of CTCF are known to differentially contribute to the CTCF-DNA interaction at different binding sites.