Date of Award
8-24-2023
Degree Name
Doctor of Philosophy (PhD)
Degree Type
Dissertation
Abstract
The regulation of gene expression relies on the complex interplay of transcription factors (TFs) that interact with DNA to control gene activity. Despite extensive research efforts, accurately predicting crucial aspects of the transcriptional process, such as TF occupancy in vivo, remains a challenging task. Existing thermodynamic models of TF function often fall short in explaining experimental observations, suggesting the presence of undiscovered biological mechanisms. This dissertation aims to unravel the underlying principles governing the binding specificity of Zinc cluster TFs and is organized into two chapters. Chapter 1 offers a comprehensive overview of transcriptional regulation in yeast, highlighting current TF binding models, and exploring various methods employed to decipher their specific binding preferences. By critically assessing the strengths and limitations of existing approaches, this chapter provides a solid foundation for investigating the binding specificity of Zinc cluster TFs. Chapter 2 delves into an in-depth analysis of Gal4, one of the most extensively studied TFs in yeast. We constructed a Shea–Ackers thermodynamic model to describe Gal4's binding behavior and compared the model's predictions with experimentally measured Gal4p binding in vivo. Surprisingly, the model failed to predict Gal4p binding at many promoters where substantial binding was observed. Further investigation revealed that these outlier promoters lacked canonical binding motifs but exhibited an unexpected binding pattern: Gal4p bound to DNA sequences with a high density of its half site (CGG). This novel mode of binding was confirmed through multiple experimental and computational approaches. Additionally, we discovered that this binding mode is frequently utilized by other Zinc cluster TFs, accounting for approximately 27% of their target sites on average. By shedding light on this previously unrecognized mode of binding, our research contributes to a deeper understanding of the fundamental principles that govern Zinc cluster TF binding specificity. Through these insights, we aim to unravel novel mechanisms underlying gene regulation and enhance our overall understanding of transcriptional regulation.
Language
English (en)
Chair and Committee
Robi Mitra
Recommended Citation
Recio, Pamela Samantha, "Unraveling the Molecular Basis of Zinc Cluster Transcription Factor Specificity: A Comprehensive Study of Half-Site Promoter Binding Interactions and their Role in Gene Expression Regulation" (2023). Arts & Sciences Electronic Theses and Dissertations. 3124.
https://openscholarship.wustl.edu/art_sci_etds/3124