Integrating space and time in patterning of gene expression in embryogenesis via a synthetic approach

During development, reproducible cell identity is established through the expression of specific genes at the correct time and correct location in space in all individuals. It remains unclear how genes extract and combine both positional and temporal information from different transcription factor (TF) profiles along embryo or tissue axes. Here, we showcase the classic hunchback gene, with focus on 3 of its main TFs during Drosophila early embryogenesis: Bicoid, Zelda and Hunchback proteins. We constructed a series of synthetic ms2 reporters, where the numbers of binding sites for each TF are varied systematically. Using live-imaging of transcription dynamics by these synthetic reporters and modeling tools, we show that Bicoid and Zelda act as sources of positional information for gene expression. Notably, they are found to regulate in synergy the same steps in transcription initiation. Meanwhile, the Hunchback protein, which constitutes a feedback on the hunchback gene expression, targets the downstream steps of the transcription process, independent of Bicoid and Zelda. With the regulatory mechanisms of individual TFs identified, we hope to shed light on when and how robust cell identity can be established from the dynamical gap genes patterns