Stripe forming architecture of the gap gene system

In this report, we show that gap genes encode exactly one set of pair-rule stripes, which occur in the native even-skipped position. The core of this work is a detailed analysis that shows how this conclusion follows from the arrangement of gap domains in the embryo. This analysis shows that: (1) pattern forming information is transmitted from gap to pair-rule genes by means of a nonredundant set of morphogenetic gradients, and (2) the stripe forming capability of the gap genes is constrained by the arrangement of these gradients and by the fact that each gap domain consists of a pair of correlated gradients. We also show that in the blastoderm, the regulatory sign of a transcriptional regulator is unlikely to change in a concentration dependent manner. The principal analytic tool used to establish these results is the gene circuit method. Here, this method is applied to examine hybrid data sets consisting of real gene expression data for four gap genes and hypothetical pair-rule expression data generated by translating native even-skipped data along the anterior-posterior axis. In this way, we are able to investigate the stripe forming capabilities of the gap gene system in the complete absence of pair-rule cross regulation. We close with an inference about evolutionary development. It is argued that the constraints on gap gene architecture identified here are a consequence of selective pressures that minimize the number of gap genes required to determine segments in long-germ band insects.