Deepika Gunasekaran will be giving a practice talk for her defense.
Title: "Evolution of the gene regulatory network controlling biofilm formation in Candida species"
Abstract: Gene expression is one of the most fundamental processes in a cell, allowing genetic information to be processed into functional products. Regulation of gene expression is determined by the underlying gene regulatory networks (GRNs). We can think of a GRN as a directed network with hub nodes denoting DNA-binding proteins and target nodes denoting downstream genes whose expression is modulated. The directed network edges denote strength of the interaction between the DNA-binding proteins and downstream target genes. High-throughput genomic and epigenetic data is used to construct GRNs and to estimate the robustness of these networks. In my study, I used a GRN underlying the formation of complex multicellular structures called biofilms, in the yeast species Candida albicans. I developed three tools to infer the structure of GRNs across Candida species, identify mutations in the C. albicans population that affect the network components, and estimate the evolutionary forces acting on the components of the biofilm GRN. Using these tools, I found that the motif preferences of the DNA-binding proteins are conserved across large evolutionary distances but their interaction with target genes is highly divergent. This is driven in part by mutations resulting in gains and losses of genomic regions where the DNA-binding proteins preferentially bind. Additionally, mutations accumulate in segments of DNA-binding proteins that are required to interact with other hub proteins in the network. This affects the overall structure of the network both within and between species.
