title: GBshape: a genome browser database for DNA shape annotations.
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 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.
authors.affiliation: Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA.
authors.forename: Tsu-Pei
authors.initials: TP
authors.lastname: Chiu
authors.affiliation: Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA.
authors.forename: Lin
authors.initials: L
authors.lastname: Yang
authors.affiliation: Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA.
authors.forename: Tianyin
authors.initials: T
authors.lastname: Zhou
authors.affiliation: Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA.
authors.forename: Bradley J
authors.initials: BJ
authors.lastname: Main
authors.affiliation: Departments of Computational Medicine and Bioinformatics and Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA.
authors.forename: Stephen C J
authors.initials: SC
authors.lastname: Parker
authors.affiliation: Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA.
authors.forename: Sergey V
authors.initials: SV
authors.lastname: Nuzhdin
authors.affiliation: Department of Chemistry and Program in Bioinformatics, Boston University, Boston, MA 02215, USA.
authors.forename: Thomas D
authors.initials: TD
authors.lastname: Tullius
authors.affiliation: Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA Departments of Chemistry, Physics, and Computer Science, University of Southern California, Los Angeles, CA 90089, USA rohs@usc.edu.
authors.forename: Remo
authors.initials: R
authors.lastname: Rohs
mesh_terms: D000818:Animals; D001665:Binding Sites; D004247:DNA / Q000737:chemistry*; D030561:Databases, Nucleic Acid; D016678:Genome; D006801:Humans; D058977:Molecular Sequence Annotation; D009690:Nucleic Acid Conformation; D009707:Nucleosomes / Q000378:metabolism; D024363:Transcription Initiation Site; D064878:Web Browser
chemical_list: D009707:Nucleosomes; D004247:DNA