This thesis investigates how pairwise combinatorial gene and stimulus perturbation experiments are conducted and interpreted. In particular, I investigate gene perturbation in the form of knockout, which can be achieved in a pairwise manner by SGA or CRISPR/Cas9 methods. In the present literature, I distinguish two approaches to interpretation: the calculation of stimulus and gene interactions, and the identification of equality among phenotypes measured for distinct perturbation conditions. I describe how each approach has been applied to derive hypotheses about gene regulatory networks. I identify conflicts and uncertainties in the assumptions allowing these derivations, and explore theoretically and experimentally approaches to improve the interpretation of genetic interaction data. I apply the approaches to a well-studied gene regulatory branch of the DNA damage checkpoint (DDC) pathway of Saccharomyces cerevisiae, and confirm the known order of genes within this pathway. I also describe observations that seem inconsistent with this pathway structure. I explore this inconsistency experimentally and discover that high concentrations of the DNA alkylating drug methyl methanesulfonate cause a cell division arrest program distinct from a G1 or G2/M checkpoint or from DNA damage adaptation, that resembles an endocycle.
| Identifer | oai:union.ndltd.org:uottawa.ca/oai:ruor.uottawa.ca:10393/37031 |
| Date | January 2017 |
| Creators | Phenix, Hilary |
| Contributors | Kærn, Mads |
| Publisher | Université d'Ottawa / University of Ottawa |
| Source Sets | Université d’Ottawa |
| Language | English |
| Detected Language | English |
| Type | Thesis |
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