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Nucleic Acids Res. 2014 Jan;42(Database issue):D148-55. doi: 10.1093/nar/gkt1087. Epub 2013 Nov 7.

TFBSshape: a motif database for DNA shape features of transcription factor binding sites.

Author information

1
Molecular and Computational Biology Program, University of Southern California, Los Angeles, CA 90089, USA, Department of Biology, Technion - Israel Institute of Technology, Technion City, Haifa 32000, Israel, Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, BC, Canada and Institute for Genome Sciences & Policy, Duke University, Durham, NC 27708, USA.

Abstract

Transcription factor binding sites (TFBSs) are most commonly characterized by the nucleotide preferences at each position of the DNA target. Whereas these sequence motifs are quite accurate descriptions of DNA binding specificities of transcription factors (TFs), proteins recognize DNA as a three-dimensional object. DNA structural features refine the description of TF binding specificities and provide mechanistic insights into protein-DNA recognition. Existing motif databases contain extensive nucleotide sequences identified in binding experiments based on their selection by a TF. To utilize DNA shape information when analysing the DNA binding specificities of TFs, we developed a new tool, the TFBSshape database (available at http://rohslab.cmb.usc.edu/TFBSshape/), for calculating DNA structural features from nucleotide sequences provided by motif databases. The TFBSshape database can be used to generate heat maps and quantitative data for DNA structural features (i.e., minor groove width, roll, propeller twist and helix twist) for 739 TF datasets from 23 different species derived from the motif databases JASPAR and UniPROBE. As demonstrated for the basic helix-loop-helix and homeodomain TF families, our TFBSshape database can be used to compare, qualitatively and quantitatively, the DNA binding specificities of closely related TFs and, thus, uncover differential DNA binding specificities that are not apparent from nucleotide sequence alone.

PMID:
24214955
PMCID:
PMC3964943
DOI:
10.1093/nar/gkt1087
[Indexed for MEDLINE]
Free PMC Article

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