GBshape: A genome browser database for DNA shape annotations

Tsu Pei Chiu, Lin Yang, Tianyin Zhou, Bradley Main, Stephen C.J. Parker, Sergey V. Nuzhdin, Thomas D. Tullius, Remo Rohs

Research output: Contribution to journalArticle

30 Scopus citations

Abstract

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 finetunes 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. GB-shape 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 Drosophilaspecies.

Original languageEnglish (US)
Pages (from-to)D103-D109
JournalNucleic Acids Research
Volume43
Issue numberD1
DOIs
StatePublished - Jan 28 2015
Externally publishedYes

ASJC Scopus subject areas

  • Genetics

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  • Cite this

    Chiu, T. P., Yang, L., Zhou, T., Main, B., Parker, S. C. J., Nuzhdin, S. V., Tullius, T. D., & Rohs, R. (2015). GBshape: A genome browser database for DNA shape annotations. Nucleic Acids Research, 43(D1), D103-D109. https://doi.org/10.1093/nar/gku977