Cell
Volume 128, Issue 6, 23 March 2007, Pages 1231-1245
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Analysis of the Vertebrate Insulator Protein CTCF-Binding Sites in the Human Genome

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Summary

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.

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Present address: Department of Genetics, Yale University School of Medicine, 333 Cedar Street, SHMI 142B, P.O. Box 208005, New Haven, CT 06120-8005, USA.