UC Irvine

ABSTRACT OF THE DISSERTATIONMechanisms of robustness and competition in transcriptional control By Rachel Victoria Waymack Doctor of Philosophy in Developmental and Cell Biology University of California, Irvine, 2021 Assistant Professor Zeba Wunderlich, Chair

During normal development, organisms must establish and maintain precise patterns of gene expression that are also robust to internal and external perturbations. The key cell fate decisions made during early development that establish the organism’s body plan rely on these precise gene expression patterns and even relatively minor deviations can cause significant defects. This precision and robustness must be achieved in the context of the inherently noisy process of transcription, which is controlled by the stochastic molecular interactions between DNA, transcription factors (TFs), and the other pieces of the transcriptional machinery. While the question of how regulatory regions of DNA, such as enhancers, accurately interact with TFs to control gene expression has been the topic of many studies, there is still much we do not know about how enhancers and TFs combine to regulate gene expression. Here, I investigate novel mechanisms of gene expression regulation by enhancers and TFs. In Chapter 2, I show that shadow enhancers, groups of seemingly redundant enhancers, are able to buffer fluctuations in upstream regulators by separating TF inputs between individual enhancers in a case study of the shadow enhancers regulating Kruppel expression during early embryonic Drosophila development. In Chapter 3, I investigate competition observed between transcriptional reporters and find that transgenic reporters compete with one another and an endogenous gene for TF activation, likely due to the non-homogenous nature of the nucleus. Then, complementing my findings in Chapter 2, I analyze the TF regulation of a large set of Drosophila shadow enhancers and show that these groups of enhancers display a wide range of regulatory logic configurations in Chapter 4. In Chapter 5, I discuss a proposed project to investigate the relationship between TF dynamics and enhancer-controlled transcription during NF-kB signaling in the immune response. Taken together, these projects inform our understanding of how gene expression is regulated by enhancers and TFs in early development and novel regulatory mechanisms that likely apply more broadly throughout the genome and life stages.