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

27 Citations (Scopus)

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

Fingerprint

Nucleic Acid Databases
Genome
DNA
Nucleosomes
Transcription Initiation Site
DNA-Binding Proteins
Periodicity
Diptera
Hydroxyl Radical
Chromatin
Transcription Factors
Nucleotides
Binding Sites
Proteins

ASJC Scopus subject areas

  • Genetics

Cite this

Chiu, T. P., Yang, L., Zhou, T., Main, B., Parker, S. C. J., Nuzhdin, S. V., ... 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

GBshape : A genome browser database for DNA shape annotations. / Chiu, Tsu Pei; Yang, Lin; Zhou, Tianyin; Main, Bradley; Parker, Stephen C.J.; Nuzhdin, Sergey V.; Tullius, Thomas D.; Rohs, Remo.

In: Nucleic Acids Research, Vol. 43, No. D1, 28.01.2015, p. D103-D109.

Research output: Contribution to journalArticle

Chiu, TP, Yang, L, Zhou, T, Main, B, Parker, SCJ, Nuzhdin, SV, Tullius, TD & Rohs, R 2015, 'GBshape: A genome browser database for DNA shape annotations', Nucleic Acids Research, vol. 43, no. D1, pp. D103-D109. https://doi.org/10.1093/nar/gku977
Chiu TP, Yang L, Zhou T, Main B, Parker SCJ, Nuzhdin SV et al. GBshape: A genome browser database for DNA shape annotations. Nucleic Acids Research. 2015 Jan 28;43(D1):D103-D109. https://doi.org/10.1093/nar/gku977
Chiu, Tsu Pei ; Yang, Lin ; Zhou, Tianyin ; Main, Bradley ; Parker, Stephen C.J. ; Nuzhdin, Sergey V. ; Tullius, Thomas D. ; Rohs, Remo. / GBshape : A genome browser database for DNA shape annotations. In: Nucleic Acids Research. 2015 ; Vol. 43, No. D1. pp. D103-D109.
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