Disease relevance of CTCF

• Reciprocal binding of CTCF and BORIS to the NY-ESO-1 promoter coincides with derepression of this cancer-testis gene in lung cancer cells [1].
• Our results identify CTCF as a novel epigenetic regulator of the human retinoblastoma gene promoter [2].
• Loss of imprinting of insulin-like growth factor-II in Wilms' tumor commonly involves altered methylation but not mutations of CTCF or its binding site [3].
• In one of four analyzed paired DNA samples from primary breast cancer patients, we have detected a tumor-specific rearrangement of CTCF exons encoding the 11-zinc-finger domain [4].
• A widely expressed transcription factor with multiple DNA sequence specificity, CTCF, is localized at chromosome segment 16q22.1 within one of the smallest regions of overlap for common deletions in breast and prostate cancers [4].

High impact information on CTCF

• In vertebrates, insulator's function requires association with the CCCTC-binding factor (CTCF), a protein that recognizes long and diverse nucleotide sequences [5].
• The majority of them fit to a consensus motif highly conserved and suitable for predicting possible insulators driven by CTCF in other vertebrate genomes [5].
• Here, we describe 13,804 CTCF-binding sites in potential insulators of the human genome, discovered experimentally in primary human fibroblasts [5].
• Using ChiP-Seq-technology, the number of binding sites was increased to 26,814, also revealing a modified consensus sequence found in 95% of the sites [6]
• 5. Here we show that inherited microdeletions in the H19 differentially methylated region (DMR) that abolish two CTCF target sites cause this disease [7].
• An insulator trap assay showed that the insulator function of most of these CTCF target sites is sensitive to 3-aminobenzamide, an inhibitor of poly(ADP-ribose) polymerase activity [8].

Chemical compound and disease context of CTCF

• We describe a 2.2-kbp microdeletion in the H19/insulin-like growth factor 2 (IGF2)-imprinting center eliminating three target sites of the chromatin insulator protein CTCF that we believe here is necessary, but not sufficient, to cause BWS and Wilms' tumor [9].

Biological context of CTCF

• Methylation of a CTCF-dependent boundary controls imprinted expression of the Igf2 gene [10].
• Furthermore, we show that CTCF, a zinc finger protein implicated in vertebrate boundary function, binds to several sites in the unmethylated imprinted-control region that are essential for enhancer blocking [11].
• Consistent with our model, CTCF binding is abolished by DNA methylation [11].
• Methylation of CpGs within the CTCF-binding sites eliminates binding of CTCF in vitro, and deletion of these sites results in loss of enhancer-blocking activity in vivo, thereby allowing gene expression [10].
• Here we show that in contrast to other zinc-finger proteins, CTCF indeed is bound to mitotic chromosomes [12].

Anatomical context of CTCF

• These results demonstrate that CTCF is a common determinant to different pathways of death signaling in immature B cells [13].
• CT genes are normally expressed in BORIS-positive male germ cells deficient in CTCF and meCpG contents, but are strictly silenced in somatic cells [1].
• 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 [14].
• The insulator binding protein CTCF associates with the nuclear matrix [15].
• In all cell lines analyzed, including cells of lung, renal, monocytic and T-cell origin, the IRAK2 luciferase reporter construct, containing an intact CTCF-binding site, showed strong promoter activity [16].

Associations of CTCF with chemical compounds

• Activation of the endogenous CTCF locus by BCR ligation was also mimicked by three other routes to apoptotic death in WEHI 231: inhibition of the phosphoinositide 3-kinase or mTORFRAP signaling cascades and treatment with transforming growth factor (TGF)-beta [13].
• We demonstrate that CTCF is associated with the nuclear matrix and can be cross-linked to DNA by cisplatin, an agent that preferentially cross-links nuclear matrix proteins to DNA in situ [15].
• Chromatin immunoprecipitation (ChIP) assays indicate an increase of lysine 4 methylation (dimethyl Lys4-H3) on the paternal chromatin and a gain in lysine 9 methylation (trimethyl Lys9-H3) on the maternal chromatin at the same CTCF-binding site [17].
• We propose a model in which incomplete gain or loss of methylation at this CTCF-binding site during tumorigenesis explains the complex and often conflicting expression patterns of IGF2 and H19 in tumors [18].
• Thyroid hormone-regulated enhancer blocking: cooperation of CTCF and thyroid hormone receptor [19].

Physical interactions of CTCF

• This assay revealed a CTCF-binding site within the mouse Irak2 promoter [16].
• Identification, genome mapping, and CTCF binding of potential insulators within the FXYD5-COX7A1 locus of human Chromosome 19q13.12 [20].
• CTCF binds to a number of important regulatory regions within the 5' noncoding sequence of the human MYC oncogene, and it can regulate its transcription in several experimental systems [4].
• DNA methylation in the CTCF-binding site I and the expression pattern of the H19 gene: does positive expression predict poor prognosis in early stage head and neck carcinomas [21]?
• Here we identify two CTCF-binding sites that flank the CTG repeat and form an insulator element between DMPK and SIX5 [22].

Regulatory relationships of CTCF

• Our data suggest a novel mechanism for IGF2 imprinting regulation, that is, the reduction of CTCF expression in the control of IGF2 imprinting [14].
• Transcriptional regulator CTCF controls human interleukin 1 receptor-associated kinase 2 promoter [16].
• These results demonstrate that CTCF activates transcription from the APP promoter and that the activation domain is located on the N-terminal side of the zinc finger domain [23].
• A region to the N-terminal side of the CTCF zinc finger domain is essential for activating transcription from the amyloid precursor protein promoter [23].
• CTCF regulates growth and erythroid differentiation of human myeloid leukemia cells [24].

Other interactions of CTCF

• The presence of the CTCF protein in human IRAK2 promoter was confirmed by chromatin immunoprecipitation assay [16].
• This site interacts with the zinc finger nuclear factor CTCF, involved in APP transcriptional activity [25].
• The present studies demonstrate that BCR ligation of WEHI 231 as well as of normal immature B cells greatly increased expression of CTCF in association with down-regulation of MYC followed by growth arrest and cell death [13].
• Rapid activation of CTCF by BCR ligation or treatment with TGF-beta was suppressed by ligation of CD40 [13].
• Insertional mutagenesis in combination with episomal assays identified nucleosome positioning sequences (NPSs) that set the stage for the remarkably precise distribution of the four target sites for the chromatin insulator protein CTCF to nucleosome linker sequences in the H19 ICR [26].

Analytical, diagnostic and therapeutic context of CTCF

• An electrophoretic mobility shift assay of the DNA fragments containing the IRAK2 CpG island, revealed a single high-affinity binding site for the transcriptional regulator and a chromatin insulator protein, CTCF [16].
• Using chromatin immunoprecipitation and PCR, we show that in several normal and neoplastic human tissues, CTCF consistently binds unmethylated ICR elements, but CTCF binding does not result in predictable gene expression [27].
• Southern blot analyses and fluorescence in situ hybridization (FISH) with normal human metaphase chromosomes showed that the human CTCF is a single-copy gene situated at chromosome locus 16q22 [4].
• To identify such proteins, we developed an affinity chromatography method based on matrix-immobilized purified recombinant CTCF [28].
• The endogenous CTCF migrates as a 130 kDa (CTCF-130) protein on SDS-PAGE, however, the open reading frame (ORF) of the CTCF cDNA encodes only a 82 kDa protein (CTCF-82) [29].

References