Characterization of the functional relevance of intranuclear transcription factor aggregates in living fly embryos

Gene expression is driven by complex interactions of transcription factor (TF) molecules with the regulatory sequences of the DNA. Recent studies have pointed towards the existence of subnuclear micro-environments, rich in TF molecules, associated with active transcription sites. However, the underlying functional implications of such TF aggregation remain to be discovered. Here, we employ live imaging and quantitative analyses in early fly embryos to visualize and characterize such TF aggregates and simultaneously measure target gene activity. We show that the micro-environment of an actively expressing gene locus is strongly associated with TF aggregation and that their respective fluctuations correlate significantly. In addition, we test the influence of specific DNA regulatory sequences on the physical characteristics of the TF aggregates. Again, we observe significant correlations between strong TF DNA binding sites, aggregate formation, and transcriptional output. Using a mathematical model we explore how these molecular TF aggregates might stabilize gene activity and thus provide precision to gene regulation.