Ctcf. Medical search. Frequent questions

In addition CTCF binding sites act as nucleosome positioning anchors so that, when used to align various genomic signals, multiple flanking nucleosomes can be readily identified. (wikipedia.org)
These results indicate that astrocyte response to elevated dopamine involves PARP1-mediated CTCF genomic restructuring and concerted expression of gene networks. (jneurosci.org)
function, we can compare CTCF motif orientations between pairs of genomic regions that are 1) connected by loops, 2) not connected by loops, 3) randomly chosen, or 4) not connected by loops, but matched for the strength of CTCF sites and distance between loop anchors. (bioconductor.org)
CTCF defines an AnnotationHub resource representing genomic coordinates of FIMO -predicted CTCF binding sites for human and mouse genomes, including the Telomere-to-Telomere and mm39 genome assemblies. (bioconductor.org)
Cohesin frequently colocalizes with CTCF (CCCTC-binding factor), affecting genomic stability, expression and epigenetic homeostasis. (scilifelab.se)

Although this property has been observed across distantly related metazoan phyla 10 , it is especially important in mammals, where CTCF knockdown leads to widespread loop disruption and gene dysregulation 15 . (nature.com)
Nevertheless, other research demonstrate unlike the pro-apoptotic function of CTCF that knockdown and over-expression of CTCF in breasts cancer cells bring about triggering apoptosis and safeguarding ectopic appearance of Bax-induced apoptosis, respectively [18]. (opioid-receptors.com)
Importantly, we revealed a hierarchical radial pattern of RFi propagation dynamics that reverses directionality from early to late S-phase and is diminished upon caffeine treatment or CTCF knockdown. (bvsalud.org)

CTCF/cohesin-binding sites are frequently mutated in cancer. (scilifelab.se)
Cohesin subunits are mutated in cancer, but CTCF/cohesin-binding sites (CBSs) in DNA have not been examined for mutations. (scilifelab.se)

The aim of this thesis is to investigate the different functions of CTCF by a combined analysis of CTCF-interacting proteins and by deletion of CTCF in vivo and in vitro. (eur.nl)
The full-size grayscale TIFF image of each main figure panel in the manuscript 'CTCF DNA binding domain undergoes dynamic and selective protein-protein interactions ' Our results reveal an interesting phenomenon in which CTCF DBD interacts with insulator proteins and selectively localizes to nuclear positions with lower concentrations of transcriptional activators, providing insights into the insulation function of CTCF. (mendeley.com)
CTCF, a nuclear transcriptional element, is really a multifunctional proteins and involves rules of development element- and cytokine-induced cell proliferation/differentiation. (opioid-receptors.com)
CTCF is one of the main architecture proteins in higher eukaryotes, and in combination with other architecture proteins and regulators, also shapes the three-dimensional organization of a genome. (biomedcentral.com)
Chromatin is made up of CTCF and other proteins, along with DNA and RNA. (sciencedaily.com)

Binding of targeting sequence elements by CTCF can block the interaction between enhancers and promoters, therefore limiting the activity of enhancers to certain functional domains. (wikipedia.org)

CTCF binds together strands of DNA, thus forming chromatin loops, and anchors DNA to cellular structures like the nuclear lamina. (wikipedia.org)
In a recent study, it has been shown that, in addition to demarcating TADs, CTCF mediates promoter-enhancer loops, often located in promoter-proximal regions, to facilitate the promoter-enhancer interactions within one TAD. (wikipedia.org)
CTCF physically binds to itself to form homodimers, which causes the bound DNA to form loops. (wikipedia.org)
It is currently believed that the DNA loops are formed by the "loop extrusion" mechanism, whereby the cohesin ring is actively being translocated along the DNA until it meets CTCF. (wikipedia.org)
function to test the "covergence rule" of CTCF-bound chromatin loops, first described in Rao et al. (bioconductor.org)
The anchors of these loops are bound by the protein CTCF, which is required for loop formation and maintenance. (bioconductor.org)
That is, CTCF binding motifs found at the anchors of loops tend to be oriented towards the center of the loop more often then would be expected by chance. (bioconductor.org)
It was initially discovered by first filtering for loops that had a single CTCF binding site at each end of the loop. (bioconductor.org)
In mammals, the CTCF protein defines the boundaries of most chromatin loops, and variations in CTCF occupancy are associated with looping divergence. (nature.com)
We demonstrate that TE-derived CTCF binding divergence may explain a large fraction of variable loops. (nature.com)
In order for a protein called CTCF to make loops in the DNA, we discovered that it needs to have hemimethylated DNA close by," says Emory biologist Victor Corces, whose lab conducted the research. (sciencedaily.com)
The researchers found that hemimethlyation only occurs near the binding sites of CTCF -- the main protein involved in organizing DNA into loops. (sciencedaily.com)
If we got rid of the hemimethlyation, CTCF did not make loops," Corces says. (sciencedaily.com)
Somehow, hemimethylation is allowing CTCF to make loops. (sciencedaily.com)
The structural basis for cohesin-CTCF-anchored loops. (nih.gov)

In recent studies, CTCF binding loss is reported to increase localized CpG methylation, which reflected another epigenetic remodeling role of CTCF in human genome. (wikipedia.org)
CTCF) are short handed, the epigenetic weeds tend to get unruly. (epigenie.com)
This report establishes CTCF as a notable tumour-suppresor and hints that the epigenetic stability caused by it is a major roadblock to cancer progression. (epigenie.com)
Here, we have identified a CTCF binding site that functions as an epigenetic barrier site in the HOXA locus. (yale.edu)
In addition, CTCF may be the main component of the heritable epigenetic system, regulating the interplay between DNA methylation, nuclear architecture, and lineage-specific gene expression. (biomedcentral.com)

Transcriptional repressor CTCF also known as 11-zinc finger protein or CCCTC-binding factor is a transcription factor that in humans is encoded by the CTCF gene. (wikipedia.org)
CTCF is involved in many cellular processes, including transcriptional regulation, insulator activity, V(D)J recombination and regulation of chromatin architecture. (wikipedia.org)
A subset of evolutionarily young sites may harbour transcriptional functionality as evidenced by the stability of their binding across multiple tissues in M. musculus domesticus (BL6), while overall the distance of subspecies-specific CTCF binding to the nearest transcription start sites and/or topologically associated domains (TADs) is largely similar to musculus-common CTCF sites. (cam.ac.uk)
In contrast to CTCF we found CTCFL highly enriched at 'open' chromatin marked by H3K27 acetylation, H3K4 di- and trimethylation, H3K79 dimethylation and H3K9 acetylation plus the histone variant H2A.Z. CTCFL is enriched at transcriptional start sites and regions bound by transcription factors. (eur.nl)
Our data indicate that activation of retroelements has produced species-specific expansions of CTCF binding in rodents, dogs, and opossum, which often functionally serve as chromatin and transcriptional insulators. (scilifelab.se)
A FDR corrected p-value of 0.05 was applied as the cut off to identify differentially regulated transcripts Results: We could show that MO assisted depletion of Rad21 and CTCF affected the transcriptional profiles of embryos in different ways. (refine.bio)

This is in line with the concept that a subpopulation of CTCF associates with the RNA polymerase II (Pol II) protein complex to activate transcription. (wikipedia.org)
The protein CTCF plays a heavy role in repressing the insulin-like growth factor 2 gene, by binding to the H-19 imprinting control region (ICR) along with differentially-methylated region-1 (DMR1) and MAR3. (wikipedia.org)
We further show that this plasticity depends on activation of genes sensitive to DNA-binding protein CTCF. (jneurosci.org)
CTCF is a protein that mediates distinct processes of gene regulation, including transcription and the structural organization of the genome. (eur.nl)
The CCCTC-binding factor (CTCF) is a highly conserved insulator protein that plays various roles in many cellular processes. (biomedcentral.com)
It is possible that CTCF, through using different combinations of zinc fingers, interacting with different protein partners, and the last but not the least, employing various post-translational modifications, could mediate extensive intra- and inter-chromatin interactions [ 7 , 8 ]. (biomedcentral.com)
However, changes of CTCF-binding sites during the cell cycle, and functions of this protein at different cell cycle phases, remain largely uncharacterized. (biomedcentral.com)
Research suggests that some disorders are associated with CTCF binding -- either mutations in the protein itself or with the DNA sequence where the protein binds," Corces says. (sciencedaily.com)

Loop competition and extrusion model predicts CTCF interaction specificity. (hopkinsmedicine.org)

To isolate possible mechanisms underlying these structural and functional changes, we used whole-genome RNA sequencing and found prominent dopamine-induced enrichment of genes containing the CCCTC-binding factor (CTCF) motif, suggesting involvement of chromatin restructuring in the nucleus. (jneurosci.org)
CTCF binds a specific non-palindromic DNA sequence motif. (bioconductor.org)
package which contains features from the GM12878 cell line aligned to hg19 as well as CTCF motif data from the CTCF data package available on Bioconductor. (bioconductor.org)
To gain insight into how these DNA elements are conserved and spread through the genome, we defined the full spectrum of CTCF-binding sites, including a 33/34-mer motif, and identified over five thousand highly conserved, robust, and tissue-independent CTCF-binding locations by comparing ChIP-seq data from six mammals. (scilifelab.se)

Furthermore the characteristics of CTCF and its homolog CTCFL are described in detail. (eur.nl)
The two paralogous zinc finger factors CTCF and CTCFL differ in expression such that CTCF is ubiquitously expressed, whereas CTCFL is found during spermatogenesis and in some cancer types in addition to other cell types. (eur.nl)
In addition to a chromatin-driven choice of binding sites, we determined nucleotide positions critical for DNA binding by CTCFL, but not by CTCF. (eur.nl)

Remarkably, we discovered a recurrent regulatory architecture consisting of a CTCF binding site and an interferon gene that appears to have been tandemly duplicated to create a 15-gene cluster on chromosome 4, thus forming a novel BL6 specific immune locus in which CTCF may play a regulatory role. (cam.ac.uk)
We conclude that this is a novel, CTCF binding site-dependent promoter in the HOXA locus, which generates a previously uncharacterized noncoding transcript. (yale.edu)

Methylation loss at CTCF-binding site of some genes has been found to be related to human diseases, including male infertility. (wikipedia.org)
CTCF regulates many genes very important to regulations of advancement [5, 6]. (opioid-receptors.com)
Oddly enough, the regulatory function of CTCF on its focus on genes appears generally inhibitory or insulation results, including repressing expressions of c-and genes by way of a DNA methylation-sensitive system [8, 9]. (opioid-receptors.com)
In stem cells, open chromatin participating in the most significant regression models demonstrated an enrichment for developmental genes and the TAD-forming CTCF binding complex, providing an opportunity for statistical inference of shifting TAD boundaries operating during early development. (elifesciences.org)

CTCF binding to promoter sites bidirectionally regulates gene transcription and depends on activation of poly-ADP-ribose polymerase 1 (PARP1). (jneurosci.org)
Using transient transfection assays with reporters constructs, we have determined that the sequence immediately surrounding the CTCF binding site possesses a cell-type-specific promoter activity. (yale.edu)
CTCF interacts with binding motifs upstream in the P0 promoter of gene and down-regulates appearance to control eyes advancement [11]. (opioid-receptors.com)
CTCF up-regulates PROM2 expression by binding to its promoter region. (radioloncol.com)
Coordinated cancer germline antigen promoter and global DNA hypomethylation in ovarian cancer: association with the BORIS/CTCF expression ratio and advanced stage. (uchicago.edu)

It is likely that CTCF helps to bridge the transcription factor-bound enhancers to transcription start site-proximal regulatory elements and to initiate transcription by interacting with Pol II, thus supporting a role of CTCF in facilitating contacts between transcription regulatory sequences. (wikipedia.org)
Department of Genetics, Yale University, School of Medicine, New Haven, Connecticut The multifunctional nuclear factor CTCF has been shown to regulate transcription and chromatin structure in three distinct ways. (yale.edu)
Using Rapid Amplification of cDNA Ends, we have mapped the upstream end of the transcription product, and defined a novel, putative, non-coding RNA with a transcription start site 53 base pairs downstream of the proximal side of the CTCF binding site. (yale.edu)
Here, we combine genome-wide analyses and transgenic mouse assays to dissect the regulatory logic of clustered-CCCTC-binding factor (CTCF) boundaries in vivo, interrogating their function at multiple levels: chromatin interactions, transcription and phenotypes. (mdc-berlin.de)

The human genome contains anywhere between 15,000 and 40,000 CTCF binding sites depending on cell type, suggesting a widespread role for CTCF in gene regulation. (wikipedia.org)

CTCF binds to the consensus sequence CCGCGNGGNGGCAG (in IUPAC notation). (wikipedia.org)
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. (wikipedia.org)

Western blot analysis in U-251MG cells transfected with control siRNA, target specific siRNA probe #1 and #2, using Anti-CTCF antibody. (atlasantibodies.com)
Immunofluorescence staining of MCF7 cells using the Anti-CTCF monoclonal antibody, showing specific staining in the nucleoplasm in green. (atlasantibodies.com)
CTCF antibody detects endogenous levels of total CTCF. (researchgrade.com)

The disorder is caused by heterozygous, pathogenic variants (larger deletions, truncating variants or missense variants within the zinc-finger domains) in the CTCF -gene on chromosome 16q22.1, which encodes for an important chromatin organizer. (orpha.net)

Using chromatin immuno-precipitation (ChIP) followed by ChIP-seq, it was found that CTCF localizes with cohesin genome-wide and affects gene regulatory mechanisms and the higher-order chromatin structure. (wikipedia.org)

CTCF also occurs frequently at the boundaries of sections of DNA bound to the nuclear lamina. (wikipedia.org)
On the other hand, CTCF binding may set boundaries for the spreading of DNA methylation. (wikipedia.org)

Besides acting as enhancer blocking, CTCF can also act as a chromatin barrier by preventing the spread of heterochromatin structures. (wikipedia.org)

Chromatin architecture in the fly: Living without CTCF/cohesin loop extrusion? (manchester.ac.uk)
However, whereas CTCF/cohesin loop extrusion is emerging as a key mechanism for the formation of mammalian topological domains, the genome organization in Drosophila appears to depend primarily on the partitioning of chromatin state domains. (manchester.ac.uk)
Dive into the research topics of 'Chromatin architecture in the fly: Living without CTCF/cohesin loop extrusion? (manchester.ac.uk)

The many functions of CTCF can now be viewed in the context of genome-wide analyses. (biomedcentral.com)

As evidenced by our prior studies, CTCF is certainly up-regulated by EGF-stimulated activation from the Erk signaling pathway leading to suppression of appearance during EGF-induced corneal epithelial cell proliferation [12]. (opioid-receptors.com)
The phosphorylation of CTCF is certainly connected with cell proliferation/differentiation [13, 14]. (opioid-receptors.com)

A manifestation vector comprising cDNA encoding full-length CTCF gene (referred to as pcDNA4-CTCF) was transfected into HCE cells to improve mobile CTCF expression amounts through the use of lipofection, while cells within the control group had been transfected with pcDNA4 vector just. (opioid-receptors.com)

Overall design: mRNA profiles of (2.5, 3.3, 4.5, 5.3, 10 hpf) wild type (WT) and morpholino depleted Rad21 MO (Rad21) and CTCF MO (CTCF) embryos were generated by deep sequencing, in triplicate, using Illumina HiSeq 2000. (refine.bio)

We performed a comprehensive bioinformatics analysis on public datasets of Drosophila CTCF (dCTCF). (biomedcentral.com)

This is the time of year to spruce up the garden, but a recent report has us thinking more about a DNA Methylation landscaper: CTCF . (epigenie.com)
Reduced CTCF was found to destabilize DNA methylation prior to cancerous tumor development. (epigenie.com)

CTCF is thought to be a primary part of the activity of insulators, sequences that block the interaction between enhancers and promoters. (wikipedia.org)

CCCTC-Binding factor or CTCF was initially discovered as a negative regulator of the chicken c-myc gene. (wikipedia.org)
Our goal is to study and learn more about how CTCF (CCCTC-binding factor) variants cause the features of CTCF related disorders. (emory.edu)

To be able to know how CTCF regulates the cell development and survival, it's important to further research the function of CTCF in stress-induced signaling and loss of life pathways in a variety of cell and tissues types. (opioid-receptors.com)

Superresolution imaging reveals spatiotemporal propagation of human replication foci mediated by CTCF-organized chromatin structures. (bvsalud.org)
Together with simulation and bioinformatic analyses, our findings point to a "CTCF-organized REplication Propagation" (CoREP) model, which suggests a nonrandom selection mechanism for replication activation at the sub-RD level during early S-phase, mediated by CTCF-organized chromatin structures. (bvsalud.org)
However, the role of CTCF in the maintenance and propagation of genome architectures throughout the cell cycle remains elusive. (biomedcentral.com)

CTCF binding has also been both shown to promote and repress gene expression. (wikipedia.org)
The binding of CTCF has been shown to have many effects, which are enumerated below. (wikipedia.org)
CTCF binding has been shown to influence mRNA splicing. (wikipedia.org)
More than 30,000 CTCF binding sites have been characterized. (wikipedia.org)
On the other hand, high-resolution nucleosome mapping studies have demonstrated that the differences of CTCF binding between cell types may be attributed to the differences in nucleosome locations. (wikipedia.org)
Abstract: Background: The introduction of novel CTCF binding sites in gene regulatory regions in the rodent lineage is partly the effect of transposable element expansion, particularly in the murine lineage. (cam.ac.uk)
The exact mechanism and functional impact of evolutionarily novel CTCF binding sites are not yet fully understood. (cam.ac.uk)
We investigated the impact of novel subspecies-specific CTCF binding sites in two Mus genus subspecies, Mus musculus domesticus and Mus musculus castaneus, that diverged 0.5 million years ago. (cam.ac.uk)
Results: CTCF binding site evolution is influenced by the action of the B2-B4 family of transposable elements independently in both lineages, leading to the proliferation of novel CTCF binding sites. (cam.ac.uk)
Conclusions: Our results demonstrate that thousands of CTCF binding sites show multiple functional signatures rapidly after incorporation into the genome. (cam.ac.uk)
While many CTCF binding sites fall within transposable elements (TEs), their contribution to 3D chromatin structural evolution is unknown. (nature.com)
Here we report the relative contributions of TE-driven CTCF binding site expansions to conserved and divergent chromatin looping in human and mouse. (nature.com)
While some TE-derived CTCF-binding sites may cause deleterious effects and be eliminated from the population, others may be maintained in the population as selectively neutral variants that may later be exapted for regulatory purposes, including chromatin loop anchoring. (nature.com)
Is there a role for CTCF binding sites in regulating the structure or function of the a globin gene cluster? (ox.ac.uk)
CTCF-binding locations represent regulatory sequences that are highly constrained over the course of evolution. (scilifelab.se)
We discovered fossilized repeat elements flanking deeply conserved CTCF-binding regions, indicating that similar retrotransposon expansions occurred hundreds of millions of years ago. (scilifelab.se)
Repeat-driven dispersal of CTCF binding is a fundamental, ancient, and still highly active mechanism of genome evolution in mammalian lineages. (scilifelab.se)
This activity is orientation-specific, and is dependent on an intact CTCF binding site. (yale.edu)
Individual CTCF binding site (CBS) deletions revealed that the characteristics of specific sites can outweigh other factors such as CBS number and orientation. (mdc-berlin.de)
And when CTCF makes a loop, it does so by binding ahead, going forward in the DNA sequence, they observed. (sciencedaily.com)
Butyrate induces modifications of the CTCF-binding landscape in cattle cells. (usda.gov)
Differentially CTCF-binding sites in cattle rumen tissue during weaning. (usda.gov)
We confirmed this finding with CTCF ChIP-seq that revealed strain-specific binding in the inbred founder mice. (elifesciences.org)

In lymphocyte B cells, elevated appearance of CTCF is certainly connected with down-regulation of c-resulting in cell development arrest and cell loss of life [15]. (opioid-receptors.com)

Thus, it is likely that CTCF plays a conserved role in chromatin domain organization. (biomedcentral.com)

It is unknown whether CTCF affects gene expression solely through its looping activity, or if it has some other, unknown, activity. (wikipedia.org)
Nevertheless, over-expression of CTCF in transfected HCE cells led to a counter impact against UV irradiation-induced caspase 3 activation and reduced CTCF manifestation (Fig. 2A). (opioid-receptors.com)

It also includes experimentally defined CTCF-bound cis-regulatory elements from ENCODE SCREEN . (bioconductor.org)

Mechanistically, the regulation of PROM2 by CTCF was detected by ChIP-PCR. (radioloncol.com)

Our prior research demonstrate that CTCF activity is essential for eye advancement in mice [5, 6]. (opioid-receptors.com)

Experiments show CTCF partially remains associated with chromatin during mitosis. (biomedcentral.com)

CTCF is also frequently hemizygous in human tumors. (epigenie.com)
Purified recombinant fragment of human CTCF expressed in E. Coli. (researchgrade.com)

CTCF has to be in a proper orientation to stop cohesin. (wikipedia.org)

Anatomy42

Organisms10

Diseases6

Chemicals and Drugs79

Analytical, Diagnostic and Therapeutic Techniques and Equipment27

Phenomena and Processes105

Disciplines and Occupations2

Information Science4

Health Care3

Genomic5

Knockdown3

Cohesin-bindi2

Proteins5

Targeting sequence1

Loops15

Epigenetic5

Transcriptional6

Protein8

Specificity1

Motif4

CTCFL3

Locus2

Genes4

Promoter5

Transcription4

Widespread1

Binds2

Antibody3

Zinc-finger domains1

Chromatin structure1

Boundaries2

Enhancer1

Extrusion3

Genome-wide1

Cell proliferation2

CDNA1

20001

Drosophila1

Methylation2

Interaction1

Factor2

Regulates1

Propagation3

Binding23

Lymphocyte1

Organization1

Expression2

Bound1

Regulation1

Demonstrate1

Experiments1

Human2

Orientation1