Title: DNA sequence and structure properties analysis reveals similarities and differences to promoters of stress responsive genes in Arabidopsis thaliana

Authors: Pan Zhu; Yanhong Zhou; Libin Zhang; Chuang Ma

Addresses: Hubei Bioinformatics and Molecular Imaging Key Laboratory, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China ' Hubei Bioinformatics and Molecular Imaging Key Laboratory, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China ' Hubei Bioinformatics and Molecular Imaging Key Laboratory, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China ' Hubei Bioinformatics and Molecular Imaging Key Laboratory, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China

Abstract: Understanding regulatory mechanisms of stress response in plants has important biological and agricultural significances. In this study, we firstly compiled a set of genes responsive to different stresses in Arabidopsis thaliana and then comparatively analysed their promoters at both the DNA sequence and three-dimensional structure levels. Amazingly, the comparison revealed that the profiles of several sequence and structure properties vary distinctly in different regions of promoters. Moreover, the content of nucleotide T and the profile of B-DNA twist are distinct in promoters from different stress groups, suggesting Arabidopsis genes might exploit different regulatory mechanisms in response to various stresses. Finally, we evaluated the performance of two representative promoter predictors including EP3 and PromPred. The evaluation results revealed their strengths and weakness for identifying stress-related promoters, providing valuable guidelines to accelerate the discovery of novel stress-related promoters and genes in plants.

Keywords: Arabidopsis thaliana; B-DNA twist; bioinformatics; data mining; nucleotide content; regulatory mechanisms; plant stress response; structural properties; stress responsive genes; promoter prediction; transcriptional regulation; DNA sequences; DNA structure; plants.

DOI: 10.1504/IJDMB.2015.070832

International Journal of Data Mining and Bioinformatics, 2015 Vol.13 No.1, pp.1 - 12

Received: 21 Feb 2013
Accepted: 19 Jul 2013
Published online: 30 Jul 2015 *

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