GBshape: a genome browser database for DNA shape annotations

Download/View
Nucl. Acids Re...pdf (2.107Mb)
Main article
Chiu_etal_Supp...pdf (150.1Kb)
Supplementary data
Date Issued
2014-10-17Related DOI
10.1093/nar/gku977Author
Chiu, Tsu-Pei
Yang, Lin
Zhou, Tianyin
Main, Bradley
Parker, Stephen C.J.
Nuzhdin, Sergey V.
Tullius, Thomas D.
Rohs, Remo
Metadata
Show full item recordPermanent Link
http://dx.doi.org/10.1093/nar/gku977https://hdl.handle.net/2144/9373
Citation
Chiu, Tsu-Pei, Yang, Lin, et al. "GBshape: a genome browser database for DNA shape annotations." Nucleic Acids Research, 17 October 2014. http://dx.doi.org/10.1093/nar/gku977Abstract
Many regulatory mechanisms require a high degree of specificity in protein-DNA binding. Nucleotide sequence does not provide an answer to the question of why a protein binds only to a small subset of the many putative binding sites in the genome that share the same core motif. Whereas higher-order effects, such as chromatin accessibility, cooperativity and cofactors, have been described, DNA shape recently gained attention as another feature that fine-tunes the DNA binding specificities of some transcription factor families. Our Genome Browser for DNA shape annotations (GBshape; freely available at http://rohslab.cmb.usc.edu/GBshape/) provides minor groove width, propeller twist, roll, helix twist and hydroxyl radical cleavage predictions for the entire genomes of 94 organisms. Additional genomes can easily be added using the GBshape framework. GBshape can be used to visualize DNA shape annotations qualitatively in a genome browser track format, and to download quantitative values of DNA shape features as a function of genomic position at nucleotide resolution. As biological applications, we illustrate the periodicity of DNA shape features that are present in nucleosome-occupied sequences from human, fly and worm, and we demonstrate structural similarities between transcription start sites in the genomes of four Drosophila species.