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

Kim, T. H., Abdullaev, Z. K., Smith, A. D., Ching, K. A., Loukinov, D. I., Green, R. D., Zhang, M. Q., Lobanenkov, V. V., Ren, B. (2007) Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome. Cell, 128 (6). pp. 1231-1245. ISSN 0092-8674

URL: https://www.ncbi.nlm.nih.gov/pubmed/17382889
DOI: 10.1016/j.cell.2006.12.048

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.

Item Type: Paper
Uncontrolled Keywords: ENHANCER-BLOCKING ACTIVITY C-MYC GENE TRANSCRIPTION-FACTOR X-INACTIVATION WIDE ANALYSIS DNA-SEQUENCE H19 GENE METHYLATION BOUNDARIES PROMOTERS
Subjects: bioinformatics > genomics and proteomics > genetics & nucleic acid processing > protein structure, function, modification > protein types > CCCTC-binding factor
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > Chromatin dynamics > heterochromatin
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > protein structure, function, modification > protein types > transcription factor
CSHL Authors:
Communities: CSHL labs > Zhang lab
Depositing User: CSHL Librarian
Date Deposited: 11 Nov 2011 18:56
Last Modified: 30 Mar 2018 15:02
PMCID: PMC2572726
Related URLs:
URI: http://repository.cshl.edu/id/eprint/23068

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