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Yuen-Jong Liu, An Oligonucleotide Microarray-Based Method for Determining Nucleosome Positioning in Saccharomyces cerevisiae, presented to the Department of Computer Science and the Department of Biochemical Sciences, Harvard University, 2004.

Eukaryotic DNA is packaged into nucleosomes, the basic repeating unit of chromatin. Consisting of approximately 146 base pairs wrapped around a core protein complex, nucleosomes have been shown to regulate gene expression both positively and negatively. Conventional methods to identify nucleosome positions are limited by the relatively small amount of DNA that can be assayed in one experiment. We have utilized a microarray-based technique that simultaneously measures the positions of thousands of nucleosomes across multiple genes. To facilitate the analysis of the microarray data, we developed a hidden Markov model (HMM) as an objective way to determine nucleosome positioning, thereby automatically and systematically processing DNA hybridization data on a genomic scale. I improved the HMM by incorporating the ability to simultaneously process data from multiple replicates, to consider the effects of cross-hybridization, and to ignore unusable data from poorly-hybridized microarray spots. After developing a graphical user interface for visualizing nucleosome positions, I found wide variations in nucleosome density. There was a significant difference in nucleosome density between gene-coding and intergenic regions. Though our preliminary results did not show significant correlation between transcription level and nucleosome density on promoter regions, exploration and quantification in this area is now possible.