PhD defence: Mapping Cellular Signals at Scale - A Reporter Platform for Multiplexed Detection of Transcription Factor Activity

PLEASE NOTE: If a candidate gives a layman's talk, the livestream will start fifteen minutes earlier.

Cells communicate through complex signaling networks that control how genes are turned on and off. These networks are far more intricate than the simple linear pathways often shown in textbooks. At the heart of this complexity are transcription factors (TFs) - proteins that interpret signals and regulate gene expression by binding to specific DNA sequences. Understanding how TFs respond to signals and coordinate gene activity is essential for uncovering how cells function and what goes wrong in disease.

This thesis develops and applies massively parallel reporter assays (MPRAs) to study TF activity at large scale. MPRAs make it possible to measure the activity of thousands of DNA sequences simultaneously, offering a powerful way to explore how TFs control transcription. Using this approach, we created optimized reporters that sensitively and specifically measure the activity of many TFs in parallel. These reporters were assembled into a compact “prime TF reporter” library, together with a computational analysis framework, enabling high-throughput and quantitative assessment of TF dynamics in living cells.

By benchmarking this system against existing genomic methods, we show that it provides complementary and often more direct insights into TF regulation. Beyond TFs, we also demonstrate how similar reporter-based strategies can illuminate other DNA-related processes, such as genome editing. Overall, this work advances our ability to map the flow of information from cellular signals to gene regulation, providing new tools to study signaling, transcription, and disease mechanisms.