HCSGD entry for CTCF
1. General information
| Official gene symbol | CTCF |
|---|---|
| Entrez ID | 10664 |
| Gene full name | CCCTC-binding factor (zinc finger protein) |
| Other gene symbols | |
| Links to Entrez Gene | Links to Entrez Gene |
2. Neighbors in the network
This gene isn't in Literature mining network.
3. Gene ontology annotation
GO ID | GO term | Evidence | Category |
|---|---|---|---|
| GO:0000775 | Chromosome, centromeric region | IDA | cellular_component |
| GO:0000793 | Condensed chromosome | IDA | cellular_component |
| GO:0003700 | Sequence-specific DNA binding transcription factor activity | IDA | molecular_function |
| GO:0003714 | Transcription corepressor activity | TAS | molecular_function |
| GO:0005515 | Protein binding | IPI | molecular_function |
| GO:0005634 | Nucleus | IDA | cellular_component |
| GO:0005654 | Nucleoplasm | IDA | cellular_component |
| GO:0005730 | Nucleolus | IDA | cellular_component |
| GO:0006349 | Regulation of gene expression by genetic imprinting | IEA | biological_process |
| GO:0006351 | Transcription, DNA-templated | IEA | biological_process |
| GO:0007059 | Chromosome segregation | IEA | biological_process |
| GO:0008270 | Zinc ion binding | TAS | molecular_function |
| GO:0010216 | Maintenance of DNA methylation | IEA | biological_process |
| GO:0010628 | Positive regulation of gene expression | IMP | biological_process |
| GO:0016568 | Chromatin modification | IEA | biological_process |
| GO:0016584 | Nucleosome positioning | IDA | biological_process |
| GO:0031060 | Regulation of histone methylation | IEA | biological_process |
| GO:0035065 | Regulation of histone acetylation | IEA | biological_process |
| GO:0040029 | Regulation of gene expression, epigenetic | IMP | biological_process |
| GO:0040030 | Regulation of molecular function, epigenetic | IMP | biological_process |
| GO:0043035 | Chromatin insulator sequence binding | IDA | molecular_function |
| GO:0043565 | Sequence-specific DNA binding | IDA | molecular_function |
| GO:0044212 | Transcription regulatory region DNA binding | IDA | molecular_function |
| GO:0045892 | Negative regulation of transcription, DNA-templated | IDA | biological_process |
| GO:0045893 | Positive regulation of transcription, DNA-templated | IDA IMP | biological_process |
| GO:0070602 | Regulation of centromeric sister chromatid cohesion | NAS | biological_process |
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4. Expression levels in datasets
- Meta-analysis result
| p-value up | p-value down | FDR up | FDR down |
|---|---|---|---|
| 0.3596651153 | 0.0992038714 | 0.9999902473 | 0.6031021473 |
- Individual experiment result
( "-" represent NA in the specific microarray platform )
( "-" represent NA in the specific microarray platform )
| Data source | Up or down | Log fold change |
|---|---|---|
| GSE11954 | Up | 0.1913865952 |
| GSE13712_SHEAR | Down | -0.2060950806 |
| GSE13712_STATIC | Down | -0.2755397477 |
| GSE19018 | Down | -1.1621093578 |
| GSE19899_A1 | Down | -0.3045577198 |
| GSE19899_A2 | Down | -0.1793796578 |
| PubMed_21979375_A1 | Up | 0.9613021116 |
| PubMed_21979375_A2 | Up | 0.4822076257 |
| GSE35957 | Down | -0.4265487739 |
| GSE36640 | Down | -0.8957412077 |
| GSE54402 | Up | 0.1777024567 |
| GSE9593 | Down | -0.2616069000 |
| GSE43922 | Up | 0.1874156754 |
| GSE24585 | Down | -0.1744041442 |
| GSE37065 | Up | 0.1190669422 |
| GSE28863_A1 | Up | 0.6940415978 |
| GSE28863_A2 | Up | 0.4112449577 |
| GSE28863_A3 | Down | -0.1847617036 |
| GSE28863_A4 | Up | 0.0552384155 |
| GSE48662 | Down | -0.4978233450 |
5. Regulation relationships with compounds/drugs/microRNAs
- Compounds
Not regulated by compounds
- Drugs
Not regulated by drugs
- MicroRNAs
- mirTarBase
MiRNA_name | mirBase ID | miRTarBase ID | Experiment | Support type | References (Pubmed ID) |
|---|---|---|---|---|---|
| hsa-miR-215-5p | MIMAT0000272 | MIRT024342 | Microarray | Functional MTI (Weak) | 19074876 |
| hsa-miR-192-5p | MIMAT0000222 | MIRT026312 | Microarray | Functional MTI (Weak) | 19074876 |
| hsa-miR-24-3p | MIMAT0000080 | MIRT030430 | Microarray | Functional MTI (Weak) | 19748357 |
| hsa-miR-1229-3p | MIMAT0005584 | MIRT036336 | CLASH | Functional MTI (Weak) | 23622248 |
| hsa-miR-615-3p | MIMAT0003283 | MIRT040249 | CLASH | Functional MTI (Weak) | 23622248 |
| hsa-let-7b-5p | MIMAT0000063 | MIRT052311 | CLASH | Functional MTI (Weak) | 23622248 |
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- mirRecord
No target information from mirRecord
6. Text-mining results about the gene
Gene occurances in abstracts of cellular senescence-associated articles: 5 abstracts the gene occurs.
PubMed ID of the article | Sentenece the gene occurs |
|---|---|
| 25359865 | Meanwhile, homocysteine promoted the shortening of telomere length specifically related to restoration of hTERT transcriptional expression and CCCTC-binding factor binding sites with hTERT promoter hypomethylation, as detected by quantitative real-time polymerase chain reaction, Western blot, methylation-specific polymerase chain reaction, and bisulfite sequencing assay |
| 23644601 | In contrast, the 11q TERRA promoter, which was previously shown to be bound by CCCTC-binding factor CTCF, displayed lower levels of markers of constitutive heterochromatin that did not change upon senescence, whereas levels of markers of facultative heterochromatin decreased upon senescence |
| 22340434 | Compared with growing fibroblasts, the CCCTC-binding factor CTCF is remarkably up-regulated in iPS cells with silencing of the three genes in the locus and is reversely down-regulated in OIS cells with high expression of p15(INK4b) and p16(INK4a) genes |
| 22340434 | These CTCF-enriched sites and the p16(INK4a) promoter associate to form compact chromatin loops in growing fibroblasts, while CTCF depletion disrupts the loop structure |
| 21465478 | The tumor suppressor role of CTCF |
| 21465478 | CTCF is an evolutionary conserved and ubiquitously expressed protein that binds thousands of sites in the human genome |
| 21465478 | Ectopic expression of CTCF in various normal and tumoral human cell lines inhibits cell division and clonogenicity, with the consequence to consider CTCF a potential tumor-suppressor factor |
| 21465478 | In this review article, we focused on the molecular mechanisms engaged by CTCF to modulate the expression of several key-regulators of differentiation, cellular senescence, cell cycle control and progression, whose expression is frequently altered in tumors |
| 21465478 | Moreover, we discussed common features of CTCF at each tumor-related DNA-binding sequence, such as protein-partners, post-translational modifications, and distinctive epigenetic marks establishment |
| 21465478 | The investigation of the molecular mechanisms engaged by CTCF to modulate tumor-related genes emphasizes the cell-type dependency of its tumor suppressor role |
| 21465478 | Indeed, the ability of CTCF to bind their promoters strictly depends by cell-type features as DNA methylation, BORIS-binding and post-translational modifications as PARYlation |
| 15471867 | A loss of insulin-like growth factor-2 imprinting is modulated by CCCTC-binding factor down-regulation at senescence in human epithelial cells |
| 15471867 | As a mechanism, a 2-fold decrease in the binding of the enhancer-blocking element CCCTC-binding factor (CTCF) within the intergenic IGF2-H19 region was found to underlie this switch to biallelic IGF2 expression in senescent cells |
| 15471867 | This decrease in CTCF binding was associated with reduced CTCF expression in senescent cells |
| 15471867 | No de novo increases in methylation at the IGF2 CTCF binding site were seen |
| 15471867 | The forced down-regulation of CTCF expression using small interfering RNA in imprinted prostate cell lines resulted in an increase in IGF2 expression and a relaxation of imprinting |
| 15471867 | Our data suggest a novel mechanism for IGF2 imprinting regulation, that is, the reduction of CTCF expression in the control of IGF2 imprinting |
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