CTCFBSDB 2.0: a database for CTCF-binding sites and genome organization

Nucleic Acids Res. 2013 Jan;41(Database issue):D188-94. doi: 10.1093/nar/gks1165. Epub 2012 Nov 27.

Abstract

CTCF is a highly conserved transcriptional regulator protein that performs diverse functions such as regulating gene expression and organizing the 3D structure of the genome. Here, we describe recent updates to a database of CTCF-binding sites, CTCFBSDB (http://insulatordb.uthsc.edu/), which now contains almost 15 million CTCF-binding sequences in 10 species. Since the original publication of the database, studies of the 3D structure of the genome, such as those provided by Hi-C experiments, have suggested that CTCF plays an important role in mediating intra- and inter-chromosomal interactions. To reflect this important progress, we have integrated CTCF-binding sites with genomic topological domains defined using Hi-C data. Additionally, the updated database includes new features enabled by new CTCF-binding site data, including binding site occupancy and the ability to visualize overlapping CTCF-binding sites determined in separate experiments.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Animals
  • Binding Sites
  • CCCTC-Binding Factor
  • Chromatin / chemistry
  • Databases, Genetic*
  • Dogs
  • Genome
  • Humans
  • Insulator Elements
  • Internet
  • Mice
  • Molecular Sequence Annotation
  • Nucleotide Motifs
  • Rats
  • Repressor Proteins / metabolism*
  • Transcriptome

Substances

  • CCCTC-Binding Factor
  • CTCF protein, human
  • Chromatin
  • Ctcf protein, mouse
  • Repressor Proteins