CTCFBSDB: a CTCF binding site database for characterization of vertebrate genomic insulators
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A new version of the database is available. To access it, click CTCFBSDB 2.0.
CCCTC-binding factor (CTCF) is a versatile transcription regulator that is evolutionarily conserved from fruit fly to human. CTCF binds to different DNA sequences through combinatorial use of 11-zinc fingers, and shows distinct functions (transcription activation/repression and chromatin insulation) depending on the biological contexts. CTCF is the only protein identified so far in vertebrate that binds to insulators and shows enhancer-blocking activity. In eukaryotic genomes, maintenance of distinct chromatin domains is critical for transcription control. Insulators, with the functions of enhancer-blocking and domain-bordering, are critical regulatory elements for gene expression control. They represent a class of diverged DNA sequences capable of shielding genes against inappropriate cis-regulatory signals from their genomic neighborhood. Recent studies also linked insulators to epigenetics, such as imprinting and X-chromosome inactivation. Recently, high-throughput chromatin immunoprecipitation experiments and comparative genomic studies have identified ten thousands of potential CTCFBS in the mammalian genomes. To analyze this important type of DNA regulatory elements, we created a CTCF binding site database (CTCFBSDB), a comprehensive collection of experimentally determined and computationally predicted CTCF binding sites (CTCFBS) from the literature. The database is designed to facilitate the studies on insulators and their roles in demarcating functional genomic domains.
Currently, the database contains 14155 experimentally determined and 18905 predicted CTCF binding sites. Biological knowledge and data from multiple resources were integrated to annotate the CTCF binding sites. Users can search and browse insulator sequence features, function annotations, genomic contexts including histone methylation profiles, flanking gene expression patterns and orthologous regions in other mammalian genomes. Users can also retrieve data by text search, sequence search and genomic range search. In silico prediction of CTCF binding sites in user's sequences is provided.
1. Bao L, Zhou M and Cui Y (2008) CTCFBSDB: a CTCF binding site database for characterization of vertebrate genomic insulators. Nucleic Acids Research. 36: D83-D87.