Live measurements of transcriptional bursting and dynamic gene regulation in early fly embryos*

Gene regulation is intrinsically dynamic: from the microscopic molecular events underlying transcriptional bursting, to genes cross-regulating each other in the context of a genetic network during cellular fate specification. However, knowledge about the transcriptional dynamics of individual genes and the coordinated dynamics of multiple interacting genes in their endogenous context is almost completely missing. We have developed an optimized two-photon microscope to measure real-time gene activity in early fly embryos. Our data is highly quantitative making higher-order noise and cross-correlation analysis between multiple simultaneously measured genes possible. Focusing on the gap-gene-network in the early fly embryo, we measure endogenous transcriptional output of individual, and multiple genes simultaneously to test a novel time-dependent mathematical framework for transcriptional bursting dynamics and link these to transcriptional states at the network level. We are addressing two questions in particular: What are the dynamics of transcriptional bursting for individual genes? And how do the complex out-of-equilibrium dynamics of individual genes affect the dynamics of the gene regulatory network as a whole?