Nucleic Acids Research Advance Access originally published online on November 2, 2007
Nucleic Acids Research 2008 36(Database issue):D83-D87; doi:10.1093/nar/gkm875
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Nucleic Acids Research, 2008, Vol. 36, Database issue D83-D87
© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
This article appears in the following Nucleic Acids Research issue: Database issue [View the issue table of contents]
Articles |
CTCFBSDB: a CTCF-binding site database for characterization of vertebrate genomic insulators
Department of Molecular Sciences, Center of Genomics and Bioinformatics, University of Tennessee Health Science Center, 858 Madison Avenue, Memphis, TN 38163, USA
*To whom correspondence should be addressed. Tel: +1 9014483240; Fax: +1 9014487360; Email: ycui2{at}utmem.edu
Received August 9, 2007. Revised September 30, 2007. Accepted October 1, 2007.
Recent studies on transcriptional control of gene expression have pinpointed the importance of long-range interactions and three-dimensional organization of chromatins within the nucleus. Distal regulatory elements such as enhancers may activate transcription over long distances; hence, their action must be restricted within appropriate boundaries to prevent illegitimate activation of non-target genes. Insulators are DNA elements with enhancer-blocking and/or chromatin-bordering functions. In vertebrates, the versatile transcription regulator CCCTC-binding factor (CTCF) is the only identified trans-acting factor that confers enhancer-blocking insulator activity. CTCF-binding sites were found to be commonly distributed along the vertebrate genomes. We have constructed a CTCF-binding site database (CTCFBSDB) to characterize experimentally identified and computationally predicted CTCF-binding sties. Biological knowledge and data from multiple resources have been integrated into the database, including sequence data, genetic polymorphisms, function annotations, histone methylation profiles, gene expression profiles and comparative genomic information. A web-based user interface was implemented for data retrieval, analysis and visualization. In silico prediction of CTCF-binding motifs is provided to facilitate the identification of candidate insulators in the query sequences submitted by users. The database can be accessed at http://insulatordb.utmem.edu/
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