CTCF

Transcriptional repressor CTCF also known as 11-zinc finger protein or CCCTC-binding factor is a is_associated_with::transcription factor that in humans is encoded by the CTCF is_associated_with::gene. CTCF is involved in many cellular processes, including transcriptional regulation, insulator activity, V(D)J recombination and regulation of is_associated_with::chromatin architecture.

Discovery
CCCTC-Binding factor or CTCF was initially discovered as a negative regulator of the chicken is_associated_with::c-myc gene. This protein was found to be binding to three regularly spaced repeats of the core sequence CCCTC and thus was named CCCTC binding factor.

Function
The primary role of CTCF is thought to be in regulating the 3D structure of chromatin. CTCF binds together strands of DNA, thus forming chromatin loops, and anchors DNA to cellular structures like the is_associated_with::nuclear lamina. It also defines the boundaries between active and heterochromatic DNA.

Since the 3D structure of DNA influences the regulation of genes, CTCF's activity influences the expression of genes. CTCF is thought to be a primary part of the activity of insulators, sequences that block the interaction between enhancers and promoters. CTCF binding has also been both shown to promote and repress gene expression. It is unknown whether CTCF affects gene expression solely through its looping activity, or if it has some other, unknown, activity.

Observed activity
The binding of CTCF has been shown to have many effects, which are enumerated below. In each case, it is unknown if CTCF directly evokes the outcome or if it does so indirectly (in particular through its looping role).

Transcriptional regulation
The protein CTCF plays a heavy role in repressing the is_associated_with::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.

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

Regulation of chromatin architecture
CTCF physically binds to itself to form homodimers, which causes the bound DNA to form loops. CTCF also occurs frequently at the boundaries of sections of DNA bound to the is_associated_with::nuclear lamina. Using chromatin immuno-precipitation (ChIP) followed by is_associated_with::ChIP-seq, it was found that CTCF localizes with is_associated_with::cohesin genome-wide and affects gene regulatory mechanisms and the higher-order chromatin structure.

Regulation of RNA splicing
CTCF binding has been shown to influence mRNA splicing.

DNA binding
CTCF binds to the is_associated_with::consensus sequence CCGCGNGGNGGCAG (in IUPAC notation). This sequence is defined by 11 is_associated_with::zinc finger motifs in its structure. CTCF's binding is disrupted by CpG methylation of the DNA it binds to.

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. CTCF’s ability to bind to multiple sequences through the usage of various combinations of its is_associated_with::zinc fingers earned it the status of a “multivalent protein”. More than 30,000 CTCF binding sites have been characterized. The human genome contains anywhere between 15,000-40,000 CTCF binding sites depending on cell type, suggesting a widespread role for CTCF in gene regulation. 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. 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.

Protein-protein interactions
CTCF binds to itself to form homodimers. This activity is one possibility of the mechanism of its looping activity.

CTCF has also been shown to interact with is_associated_with::Y box binding protein 1. CTCF also co-localizes with is_associated_with::cohesin, which stabilizes the repressive loops organized by the CTCF.