CBE Doctoral Dissertation Defense: “Quantitative Analysis on Enhancer-Mediated Dynamic Gene Regulations in Drosophila Embryos” (Hao Dennis Deng)

Abstract:
Proper organism development relies on precise gene regulation, where genes are expressed at specific times, locations, and quantities. Non-coding DNA sequences called enhancers play a crucial role in this process by interacting with their target promoters to initiate transcription and regulate gene expression. While the mechanisms of enhancer-mediated gene control have been extensively studied, the dynamics of the interactions between enhancers and promoters, especially within complex genomic environments, remain unclear. My research employed quantitative live cell imaging in early Drosophila embryos to explore the dynamics of enhancer-promoter interactions and their impact on gene expression, revealing several key findings. First, we observed that strong enhancer-promoter interactions induce interallelic competition such that each homozygous allele produces fewer mRNAs than the single hemizygous allele. Through systematic gene construct modulation, we found evidence suggesting that the transcription machinery binding to both enhancer and promoter regions, such as RNA Pol II and pre-initiation complex molecules, act as limiting factors that cause reduced transcription. Second, we investigated spatiotemporal thresholds of enhancer-promoter interactions required for transcription initiation and found that enhancers need to be within 500 nm of their target promoters for more than four minutes. These spatiotemporal requirements highlight the importance of sustained proximity between enhancers and target promoters in gene activation, providing insights into the mechanisms of precise gene control. Both studies support the hypothesis that transcription hubs form at regulatory elements, facilitating transcription through a local concentration of transcription machinery. These findings significantly advance our understanding of the dynamics of enhancer-promoter interplay and gene regulation at the single-cell level. The knowledge can be a foundation for precise gene control in various biological contexts, from developmental processes to potential therapeutic applications.

Zoom Link: https://upenn.zoom.us/j/94986872387?
Meeting ID: 949 8687 2387 | Passcode: 041979