Analysis of the Vertebrate Insulator Protein CTCF-Binding Sites in the Human Genome

Abstract

Insulator elements affect gene expression by preventing the spread of heterochromatin and restricting transcriptional enhancers from activation of unrelated promoters. In vertebrates, insulator's function requires association with the CCCTC-binding factor (CTCF), a protein that recognizes long and diverse nucleotide sequences. While insulators are critical in gene regulation, only a few have been reported. Here, we describe 13,804 CTCF-binding sites in potential insulators of the human genome, discovered experimentally in primary human fibroblasts. Most of these sequences are located far from the transcriptional start sites, with their distribution strongly correlated with genes. The majority of them fit to a consensus motif highly conserved and suitable for predicting possible insulators driven by CTCF in other vertebrate genomes. In addition, CTCF localization is largely invariant across different cell types. Our results provide a resource for investigating insulator function and possible other general and evolutionarily conserved activities of CTCF sites.

Epigenetic regulation of the human p53 gene promoter by the CTCF transcription factor in transformed cell lines

“…We found a putative CTCFbinding motif in a DNA fragment located at B700 bp upstream of the p53 transcription start site (Figure 3a) (De La Rosa-Vela´zquez et al, 2007;Kim et al, 2007). We performed a gel shift analysis using total extracts from HeLa cells to determine whether CTCF associates with this sequence in vitro (Figure 3b).…”

Analysis of opo cis-regulatory landscape uncovers Vsx2 requirement in early eye morphogenesis

“…This genomic area is flanked by CTCF-binding sites 50 and contains the enhancers identified in our analysis. The fact that opo and tfap2a are not separated by CTCF-binding sites and that they are both contained within the same topologically associating domain 51 open the possibility that common cis-regulatory elements may coregulate these two genes.…”

Regulation of major histocompatibility complex class II gene expression, genetic variation and disease

“…Such variation could give rise to decreased or dysregulated expression of HLA-DRB1 and HLA-DQA1 and perhaps contribute to MHC class II associations with disease. Moreover, recent genome-wide analyses of CTCF binding in human cells have identified several other CTCF-binding sites in the class II region [136][137][138] suggesting that multiple CTCF sites may serve to coordinate the expression of nearby class II genes and be candidates for the site of action of regulatory variants. …”