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Albany 2015:Book of Abstracts

Albany 2015
Conversation 19
June 9-13 2015
©Adenine Press (2012)

GBshape: a genome browser database for DNA shape annotations

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.

Reference
T. P. Chiu, et al. (2015). GBshape: a genome browser database for DNA shape annotations. Nucleic Acids Res. 43, D103-D109.

Tsu-Pei Chiu1
Lin Yang1
Tianyin Zhou1
Bradley J. Main1
Stephen C.J. Parker2
Sergey V. Nuzhdin1
Thomas D. Tullius3
Remo Rohs1

1Molecular and Computational Biology Program
Department of Biological Sciences
University of Southern California
Los Angeles, CA 90089, USA
2Departments of Computational Medicine and Bioinformatics and Human Genetics
University of Michigan
Ann Arbor, MI 48109, USA
3Department of Chemistry and Program in Bioinformatics
Boston University
Boston, MA 02215, USA

tsupeich@usc.edu