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Issue 2, 2014
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The structural properties of DNA regulate gene expression

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Abstract

Regulatory sequences such as promoters not only contain cis-regulatory elements as switches of transcription, but also exhibit particular topological features. In this paper, we introduce a systematic genome scale approach to characterize the roles of structural conformation and stability profile of promoter sequence in gene expression. The average free energy of promoter dinucleotides stacking nearest neighbors are subjected to scrutiny by statistical hidden Markov models to reveal the function of constrains and properties of promoter structure in transcription. When applied for a 1000 bp 5′ upstream sequence of genes, the proposed model via assessing free energy profile identified co-expressed genes of Arabidopsis thaliana in response to the auxin hormone. The applied perspective dynamic network which mediates transcription regulation provides a great hindrance to conceive how DNA conformation interacts with cis-regulatory elements, chromatin structure and many other factors. This study indeed drew the complexity of the promoter's regulatory behavior from sequence over the former studies and evokes a new hypothesis to be validated experimentally.

Graphical abstract: The structural properties of DNA regulate gene expression

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Publication details

The article was received on 27 Jul 2013, accepted on 21 Oct 2013 and first published on 27 Nov 2013


Article type: Paper
DOI: 10.1039/C3MB70311H
Citation: Mol. BioSyst., 2014,10, 273-280
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    The structural properties of DNA regulate gene expression

    S. Soltani, H. Askari, N. Ejlali and R. Aghdam, Mol. BioSyst., 2014, 10, 273
    DOI: 10.1039/C3MB70311H

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