Nucleosome positioning dynamics in evolution and disease
Nucleosome positioning is involved in a variety of cellular processes, and it provides a likely substrate for species evolution and may play roles in human disease. However, many fundamental aspects of nucleosome positioning remain controversial, such as the relative importance of underlying sequence features, genomic neighbourhood and trans-acting factors. In this thesis, I have focused on analyses of the divergence and conservation of nucleosome positioning, associated substitution spectra, and the interplay between them. I have investigated the extent to which nucleosome positioning patterns change following the duplication of a DNA sequence and its insertion into a new genomic region within the same species, by assessing the relative nucleosome positioning between paralogous regions in both the human (using in vitro and in vivo datasets) and yeast (in vivo) genomes. I observed that the positioning of paralogous nucleosomes is generally well conserved and detected a strong rotational preference where nucleosome positioning has diverged. I have also found, in all datasets, that DNA sequence features appear to be more important than local chromosomal environments in nucleosome positioning evolution, while controlling for trans-acting factors that can potentially confound inter-species comparisons. I have also examined the relationships between chromatin structure and DNA sequence variation, with a particular focus on the spectra of (germline and somatic) substitutions seen in human diseases. Both somatic and germline substitutions are found to be enriched at sequences coinciding with nucleosome cores. In addition, transitions appear to be enriched in germline relative to somatic substitutions at nucleosome core regions. This difference in transition to transversion ratio is also seen at transcription start sites (TSSs) genome wide. However, the contrasts seen between somatic and germline mutational spectra do not appear to be attributable to alterations in nucleosome positioning between cell types. Examination of multiple human nucleosome positioning datasets shows conserved positioning across TSSs and strongly conserved global phasing between 4 cancer cell lines and 7 non-cancer cell lines. This suggests that the particular mutational profiles seen for somatic and germline cells occur upon a common landscape of conserved chromatin structure. I extended my studies of mutational spectra by analysing genome sequencing data from various tissues in a cohort of individuals to identify human somatic mutations. This allowed an assessment of the relationship between age and mutation accumulation and a search for inherited genetic variants linked to high somatic mutation rates. A list of candidate germline variants that potentially predispose to increased somatic mutation rates was the outcome. Together these analyses contribute to an integrated view of genome evolution, encompassing the divergence of DNA sequence and chromatin structure, and explorations of how they may interact in human disease.