Published online 2 November 2007 Nucleic Acids Research, 2008, Vol. 36, Database issue D83–D87 doi:10.1093/nar/gkm875 CTCFBSDB: a CTCF-binding site database for characterization of vertebrate genomic insulators Lei Bao, Mi Zhou and Yan Cui* Department of Molecular Sciences, Center of Genomics and Bioinformatics, University of Tennessee Health Science Center, 858 Madison Avenue, Memphis, TN 38163, USA Received August 9, 2007; Revised September 30, 2007; Accepted October 1, 2007 ABSTRACT 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 compu- tationally 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/ INTRODUCTION CCCTC-binding factor (CTCF) is a versatile transcription regulator that is evolutionarily conserved from fruit ﬂy to human (1). CTCF binds to diﬀerent DNA sequences by combinatorial use of 11-zinc ﬁngers and plays a key role in many chromatin insulation events [reviewed in (2)]. In eukaryotic genomes, chromatins are organized into distinct domains. The chromatin domain architec- ture is critical for transcription control. Insulators are the key DNA sequence elements that establish and maintain such domain boundaries (2–12). They represent a class of diverged DNA sequences capable of shielding genes from inappropriate cis-regulatory signals from the genomic neighborhood. There are two types of insulators—enhancer-blocking insulators that block enhancer–promoter communication and barrier insula- tors that protect against heterochromatin-mediated silencing (13). Many recent studies have been devoted to the identiﬁcation and characterization of insulators. CTCF-binding site is of particular interest because CTCF is the only protein identiﬁed so far in vertebrate that binds to enhancer-blocking insulators and shows enhancer-blocking activity. Recent studies also linked the CTCF-binding site to epigenetic processes, such as imprinting (14–16), X-chromosome inactivation (17,18) and interchromosomal colocalization (19). Despite their obvious importance, to our knowledge, there is no public database categorizing this type of regulatory elements. In addition to dozens of well-characterized CTCF-binding sites with validated insulation functions that are scattered in the biomedical literature, several recent high-throughput ChIP-chip analyses and com- parative genomic studies (20–23) have identiﬁed tens of thousands of potential CTCF-binding sites in human and mouse genomes. Here we report our eﬀort in creating a CTCF-binding site database, a collection of experimen- tally identiﬁed and computationally predicted CTCF- binding sites. Biological knowledge and data from multiple resources were integrated to annotate the CTCF-binding sites. The database is designed to facil- itate the studies on insulators and their roles in regulating gene expression and demarcating functional genomic domains. *To whom correspondence should be addressed. Tel: +1 9014483240; Fax: +1 9014487360; Email: ycui2@utmem.edu 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.