Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome

Cell. 2007 Mar 23;128(6):1231-45. doi: 10.1016/j.cell.2006.12.048.


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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, N.I.H., Intramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Animals
  • CCCTC-Binding Factor
  • Cell Line
  • Chromatin Immunoprecipitation
  • Conserved Sequence
  • DNA-Binding Proteins / metabolism*
  • Evolution, Molecular
  • Genome, Human*
  • Humans
  • Insulator Elements / genetics*
  • Oligonucleotide Array Sequence Analysis
  • Repressor Proteins / metabolism*
  • U937 Cells
  • Vertebrates / genetics


  • CCCTC-Binding Factor
  • CTCF protein, human
  • DNA-Binding Proteins
  • Repressor Proteins

Associated data

  • GEO/GSE5559