Application of Whole Genome Sequencing and Bioinformatics Tools to Investigate Novel Interactions in DNA Repair in Drosophila melanogaster
Abstract: An organism's genome is constantly exposed to endogenous and exogenous forms of damage. If left unrepaired, DNA damage can pose a threat to the regulation and function of genes located near the site of the lesion. To address the multiple types of DNA damage that accumulate on a daily basis, organisms have evolved specific pathways to deal with each one. Although most of these pathways ha... read moreve been studied for multiple years or even decades, there are still many interactions and mechanisms that have yet to be elucidated. In recent years, the study of genomes and their maintenance has changed significantly thanks to drastic improvements to DNA sequencing technologies and the corresponding data analysis tools. In the work described here, whole genome sequencing (WGS) and bioinformatic data analysis were used to address two research questions, each of which focused on investigating DNA repair proteins and their roles in DNA repair and genomic stability in Drosophila melanogaster. First, I investigated the cause of a synthetic larval lethality, which was discovered after creating double mutants for two conserved helicases: DmBlm and DmHelQ. Second, I analyzed mutants obtained from an ethyl-methane sulfonate (EMS) mutagenesis screen that was conducted in a trans-lesion synthesis (TLS)-deficient background, in order to elucidate genes and interactions involved in the template-switching (TS) pathway of DNA damage tolerance (DDT). For both projects, I applied a single bioinformatic pipeline to WGS data, which led to the identification of strong candidates for causative variants in each.
Thesis (M.S.)--Tufts University, 2018.
Submitted to the Dept. of Biology.
Advisor: Mitch McVey.
Committee: Sergei Mirkin, Erik Dopman, and Stephen Fuchs.
Keywords: Molecular biology, Genetics, and Bioinformatics.read less