Dynamics of an incoherent feedforward loop drive ERK-dependent pattern formation in the early embryo.

Positional information in developing tissues often takes the form of stripes of gene expression that mark the boundaries of a particular cell type or morphogenetic process. How stripes form is still in many cases poorly understood. Here we use optogenetics and live-cell biosensors to investigate one such pattern: the posterior stripe of expression in the early embryo. This stripe depends on interpretation of an upstream signal - a gradient of ERK kinase activity - and the expression of two target genes and that exert antagonistic control over . We find that high or low doses of ERK signaling produce either transient or sustained expression, respectively. These ERK stimuli also regulate and expression with distinct dynamics: transcription is rapidly induced under both low and high stimuli, whereas transcription converts graded ERK inputs into an output switch with a variable time delay. Antagonistic regulatory paths acting on different timescales are hallmarks of an incoherent feedforward loop architecture, which is sufficient to explain transient or sustained dynamics and adds temporal complexity to the steady-state model of stripe formation. We further show that an all-or-none stimulus can be 'blurred' through intracellular diffusion to non-locally produce a stripe of gene expression. Overall, our study provides a blueprint for using optogenetic inputs to dissect developmental signal interpretation in space and time.