Functional Implications of Local DNA Structures in Regulatory Motifs. (14th May 2013)

• Record Type: Journal Article
• Authors: Xiang, Qian
• Other Names: Chang Hsueh-Wei Academic Editor.; Cheng Yu-Huei Academic Editor.; Liu Yunkai Academic Editor.; Yang Cheng-Hong Academic Editor.
• Is Part Of: TheScientificWorldjournal. Volume 2013(2013)
• Publication Date: 2013-05-14
• Subjects: Science -- Periodicals; Technology -- Periodicals; Medicine -- Periodicals; 505
• DOI: 10.1155/2013/965752
• Languages: English
• ISSNs: 2356-6140

Abstract

Abstract : The three-dimensional structure of DNA has been proposed to be a major determinant for functional transcription factors (TFs) and DNA interaction. Here, we use hydroxyl radical cleavage pattern as a measure of local DNA structure. We compared the conservation between DNA sequence and structure in terms of information content and attempted to assess the functional implications of DNA structures in regulatory motifs. We used statistical methods to evaluate the structural divergence of substituting a single position within a binding site and applied them to a collection of putative regulatory motifs. The following are our major observations: (i) we observed more information in structural alignment than in the corresponding sequence alignment for most of the transcriptional factors; (ii) for each TF, majority of positions have more information in the structural alignment as compared to the sequence alignment; (iii) we further defined a DNA structural divergence score (SD score) for each wild-type and mutant pair that is distinguished by single-base mutation. The SD score for benign mutations is significantly lower than that of switch mutations. This indicates structural conservation is also important for TFBS to be functional and DNA structures will provide previously unappreciated information for TF to realize the binding specificity.