mavii

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. [5][6] CTCF is involved in many cellular processes, including transcriptional regulation, insulator activity, V (D)J recombination [7] and regulation of chromatin architecture. [8]

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 promoters.

Background The CCCTC-binding factor (CTCF) has diverse regulatory functions. However, the definitive characteristics of the CTCF binding motif required for its functional diversity still remains elusive. Results Here, we describe a new motif discovery workflow by which we have identified three CTCF binding motif variations with highly divergent functionalities. Supported by transcriptomic ...

The CCCTC-binding factor (CTCF) binds tens of thousands of enhancers and promoters on mammalian chromosomes by means of its 11 tandem zinc finger (ZF) DNA-binding domain. In addition to the 12-15-bp CORE sequence, some of the CTCF binding sites contain 5' upstream and/or 3' downstream motifs. Here, we describe two structures for overlapping portions of human CTCF, respectively, including ZF1 ...

Abstract CCCTC‐binding factor (CTCF) is an eleven zinc finger (ZF), multivalent transcriptional regulator, that recognizes numerous motifs thanks to the deployment of distinct combinations of its ZFs. The great majority of the ~50,000 genomic locations bound by the CTCF protein in a given cell type is intergenic, and a fraction of these sites overlaps with transcriptional enhancers ...

A combination of microscopy and chromosome conformation capture (3C)-related approaches 2 revealed that CCCTC-binding factor (CTCF) is in large part responsible for bridging the gap between nuclear organization and gene expression. CTCF is the main insulator protein described in vertebrates.

We collected position weight matrices of CTCF binding motifs and defined strand-oriented CTCF binding sites in the human and mouse genomes, including the recent Telomere to Telomere and mm39 assemblies. We included selected experimentally determined and predicted CTCF binding sites, such as CTCF-bound cis-regulatory elements from SCREEN ENCODE.

CCCTC-binding factor (CTCF) is a conserved zinc finger transcription factor implicated in a wide range of functions, including genome organization, transcription activation, and elongation. To explore the basis for CTCF functional diversity, we coupled an auxin-induced degron system with precision nuclear run-on. Unexpectedly, oriented CTCF motifs in gene bodies are associated with ...

CTCF-binding motifs showing the M1/core that specifically engages fingers 4–8 and the M2/upstream sequence that engages fingers 7–11, with overlapping binding of the middle fingers to M1 and M2 (Nakahashi et al. 2013).

For example, DNase-I, H3K27ac, and CTCF motif binding (5′−/3′-CTCF motif) are more important for short-range interactions (0–1 Mb), whereas H3K4me3 is more important for long-range interactions (>2 M) with square root of Vanilla Coverage (SQRTVC) normalization (Supplementary Fig. 9B).

These results demonstrate the existence of definitive CTCF binding motifs corresponding to CTCF's diverse functions, and that the functional diversity of the motifs is strongly associated with genetic and epigenetic features at the 12th position of the motifs.

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.

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 consensus motif typically represented as 5′-CCACNAGGTGGCAG-3′.

CCCTC‐binding factor (CTCF) is an eleven zinc finger (ZF), multivalent transcriptional regulator, that recognizes numerous motifs thanks to the deployment of distinct combinations of its ZFs. The great majority of the ~50,000 genomic locations bound by the CTCF protein in a given cell type is intergenic, and a fraction of these sites overlaps with transcriptional enhancers. Furthermore, a ...

Thus, we propose that DNA methylation of this GC-rich motif serves as a regulatory mechanism of loop formation in M. leidyi, potentially controlling the binding of an unknown, methylation ...

The MethMotif platform integrates transcription factor binding site (TFBS) motifs with DNA methylation profiles, providing an in-depth analysis of how methylation modulates TF binding across different cell types and conditions.

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 promoters.

In mammals, most of the boundaries of topologically associating domains and all well-studied insulators are rich in binding sites for the CTCF protein. According to existing experimental data, CTCF is a key factor in the organization of the ...

Finally, by comparing changes in CTCF binding with changes in gene expression during differentiation, we show that LowOc and HighOc sites are associated with distinct regulatory functions. Our results suggest that the regulatory control of CTCF is dependent in part on specific motifs within its binding site.

Intriguingly, H3K18la also marked the long-range contact sites and particularly the CTCF-binding sites between IL1B and IL37, pointing out a possible role of histone lactylation in modifying gene architecture (Figure 6 B).