Figure 1. The gap gene system: structure, regulation, and expression.

(A) The regulatory structure of the gap gene network. Nodes represent transcription factors encoded by maternal coordinate genes bicoid (bcd, purple) and caudal (cad, cyan), as well as trunk gap genes hunchback (hb, yellow), Krüppel (Kr, green), knirps (kni, red) and giant (gt, blue). Activating interactions are indicated by arrows, repressive interactions by T-bars. Circular arrows indicate auto-activation. Dashed lines represent weak, solid lines stronger regulatory interactions. (B) Spatial representation of gap gene regulation: boxes indicate relative positions of gap domains along the antero-posterior (A–P) axis of the embryo. Anterior is to left, posterior to the right. Background colour indicates predominant activating inputs by maternal gradients. T-bars indicate gap gene cross-repression. Circular arrows represent gap gene auto-activation. (C) Gene expression dynamics of maternal coordinate genes bcd (purple) and cad (cyan), as well as trunk gap genes hb (yellow), Kr (green), kni (red) and gt (blue). Quantified expression patterns are shown as lines (maternal coordinate) and coloured areas (gap genes). Output of the fitted full model is shown as dots. Y-axes represent relative protein concentration in arbitrary units (a.u.); X-axes represent A–P position in %, where 0% is the anterior pole. C12 and C14 refer to cleavage cycle 12 and 14A, respectively. C14A is subdivided into eight time classes T1–8 of equal length. Only the trunk region of the embryo from 35 to 75% is shown. (D) Dynamical regimes driven by the gap gene system. Multistable (switch-like) behaviour in the anterior is indicated by a phase space with trajectories converging to multiple point attractors (represented by circles). Damped oscillations leading to dynamic anterior shifts of gap domains in the posterior are indicated by a colour wheel with trajectories cycling through successions of different gap genes. The bifurcation boundary between the two regimes at 52% A–P position is indicated by a dashed line. See text for details. Figure adapted from Verd et al. (2017); Verd et al. (2018).