Title
DNA structural properties in the classification of genomic transcription regulation elements DNA structural properties in the classification of genomic transcription regulation elements
Author
Faculty/Department
Faculty of Sciences. Mathematics and Computer Science
Publication type
article
Publication
Subject
Biology
Computer. Automation
Source (journal)
Bioinformatics and biology insights. - -
Volume/pages
6(2012) , p. 155-168
ISSN
1177-9322
Carrier
E
Target language
English (eng)
Full text (Publishers DOI)
Abstract
It has been long known that DNA molecules encode information at various levels. The most basic level comprises the base sequence itself and is primarily important for the encoding of proteins and direct base recognition by DNA-binding proteins. A more elusive level consists of the local structural properties of the DNA molecule wherein the DNA sequence only plays an indirect supportive role. These properties are nevertheless an important factor in a large number of biomolecular processes and can be considered as informative signals for the presence of a variety of genomic features. Several recent studies have unequivocally shown the benefit of relying on such DNA properties for modeling and predicting genomic features as diverse as transcription start sites, transcription factor binding sites, or nucleosome occupancy. This review is meant to provide an overview of the key aspects of these DNA conformational and physicochemical properties. To illustrate their potential added value compared to relying solely on the nucleotide sequence in genomics studies, we discuss their application in research on transcription regulation mechanisms as representative cases.
Full text (open access)
https://repository.uantwerpen.be/docman/irua/5baa29/492bb5fb.pdf