Computational analysis of nucleosome positioning datasets

• Main Author: Fraser, Ross Macdonald
• Published: University of Edinburgh 2006
• Subjects: 572.8
• Online Access: http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.651095

Monomer extension (ME) is an established <i>in vitro </i>experimental technique which maps the positions adopted by reconstituted core histone octamers on a defined DNA sequence. It provides quantitative positioning information, at high resolution, over long continuous stretches of DNA sequence. This technique has been employed to map several genes: globin genes (8 kbp), the beta-lactoglobulin gene (10 kbp) and various imprinting genes (4 kbp). This study explores and analyses this unique dataset, utilising computational and stochastic techniques, to gain insight into the potential influence of nucleosomal positioning on the structure and function of chromatin. The first section of this thesis expands upon prior analyses, explores general features of the dataset using common bioinformatics tools, and attempts to relate the quantitative positioning information from ME to data from other commonly used competitive reconstitution protocols. Finally, evidence of a correlation between the <i>in vitro </i>ME dataset and <i>in vivo </i>nucleosome positions for the beta-lactoglobulin gene region is presented. The second section presents the development of a novel method for the analysis of ME maps using Monte Carlo simulation methods. The goal was to use the ME datasets to simulate a higher order chromatin fibre, taking advantage of the long-range and quantitative nature of the ME datasets. The Monte Carlo simulations have allowed new insights to be gleaned from the datasets. Analysis of the beta-lactoglobulin positioning map indicates the potential for discrete disruption of nucleosomal organisation, at specific physiological nucleosome densities, over regions found to have unusual chromatin structure <i>in vivo. </i>This suggests a correspondence between the quantitative histone octamer positioning information <i>in vitro </i>and the positioning of nucleosomes <i>in vivo.</i> Taken together, these studies lend weight to the hypothesis that necleosome positioning information encoded within DNA plays a fundamental role in directing chromatin structure <i>in vivo</i>.