Illuminating the role of transcription factor dynamics in development
Understanding how genomic regulatory elements encode when and where genes are expressed in development remains one of the most important open questions in biology. Despite intense study, this knowledge gap persists because technological limitations have obscured an important degree of freedom: time. Recent discoveries made with live cell imaging have defied the textbook view of how transcription is regulated. Hence, the time is ripe to introduce a new paradigm for studying transcription in development—one based on how genes are regulated in living animals as development is actually taking place. Excitingly, we can now exploit the cutting-edge live imaging technology and quantitative approaches that I previously developed in order to visualize transcription factor (TF) concentration dynamics, transcription, and even single TF molecules in live Drosophila embryos to uncover how enhancer sequence regulates transcription in vivo.  This ambitious work will span multiple length scales, from examining changes in TF concentration at the single-nucleus level, to measuring the formation of local clusters of TFs at the locus level, to watching individual protein-protein interactions as they drive transcription at the molecular level. First, we will understand how TF concentration dynamics regulate gene expression. Second, we will uncover how recently discovered dynamic TF clusters or condensates regulate transcription and how their properties are shaped by enhancer sequence. Finally, we will overcome one of the most daunting technical challenges facing the field of transcription by developing a method to directly visualize the transient protein-protein interactions that drive transcription in vivo. Simultaneously visualizing protein-protein interactions and tracking transcription will make it possible to address the most pressing questions about transcription mechanisms in vivo, by revealing precisely when they occur and how they modulate transcription.