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Related Experiment Video

Updated: Apr 21, 2026

Analyzing and Building Nucleic Acid Structures with 3DNA

Analyzing and Building Nucleic Acid Structures with 3DNA

Published on: April 26, 2013

GBshape: a genome browser database for DNA shape annotations.

Tsu-Pei Chiu¹, Lin Yang¹, Tianyin Zhou¹

¹Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA.

Nucleic Acids Research

|October 19, 2014

Summary

This summary is machine-generated.

DNA shape, not just sequence, influences protein binding specificity. The GBshape tool visualizes and quantizes these DNA shape features across 94 genomes, aiding in understanding gene regulation.

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Area of Science:

Genomics
Structural Biology
Bioinformatics

Background:

Protein-DNA binding specificity is crucial for gene regulation.
Nucleotide sequence alone cannot fully explain binding site selection.
DNA shape is an emerging factor influencing transcription factor binding specificity.

Purpose of the Study:

To introduce GBshape, a genome browser for DNA shape annotations.
To provide genome-wide predictions of DNA shape features.
To enable visualization and download of nucleotide-resolution DNA shape data.

Main Methods:

Development of the GBshape genome browser framework.
Prediction of DNA shape features (minor groove width, propeller twist, roll, helix twist, hydroxyl radical cleavage) for 94 genomes.
Visualization of DNA shape annotations in a genome browser track format.
Download of quantitative DNA shape values.

Main Results:

GBshape provides comprehensive DNA shape annotations for numerous genomes.
Periodicity of DNA shape features in nucleosome-occupied regions was observed in human, fly, and worm.
Structural similarities in transcription start sites were identified across four Drosophila species.

Conclusions:

DNA shape is a significant determinant of protein-DNA binding specificity.
GBshape is a valuable resource for exploring genome-wide DNA shape patterns.
DNA shape analysis can reveal insights into gene regulation, nucleosome organization, and conserved genomic structures.