Genetic studies have revealed that segment determination in Drosophila melanogaster is based on hierarchical regulatory interactions among maternal coordinate and zygotic segmentation genes. The gap gene system constitutes the most upstream zygotic layer of this regulatory hierarchy, responsible for the initial interpretation of positional information encoded by maternal gradients. We present a detailed analysis of regulatory interactions involved in gap gene regulation based on gap gene circuits, which are mathematical gene network models used to infer regulatory interactions from quantitative gene expression data. Our models reproduce gap gene expression at high accuracy and temporal resolution. Regulatory interactions found in gap gene circuits provide consistent and sufficient mechanisms for gap gene expression, which largely agree with mechanisms previously inferred from qualitative studies of mutant gene expression patterns. Our models predict activation of Kr by Cad and clarify several other regulatory interactions. Our analysis suggests a central role for repressive feedback loops between complementary gap genes. We observe that repressive interactions among overlapping gap genes show anteroposterior asymmetry with posterior dominance. Finally, our models suggest a correlation between timing of gap domain boundary formation and regulatory contributions from the terminal maternal system.

Motivation: To construct an integrated map of Drosophila segmentation gene expression from partial data taken from individual embryos. Results: Spline and wavelet based registration techniques were developed to register Drosophila segmentation gene expression data. As ground control points for registration we used the locations of extrema on gene expression patterns, represented in 1D. The registration method was characterized by unprecedented high accuracy. A method for constructing the integrated pattern of gene expression at cellular resolution was designed. These patterns were constructed for 9 segmentation genes belonging to gap and pair-rule classes. Availability: Programs running on SPARC/SunOS 5.0 platform or Alpha/DU 4.0E systems may be obtained from the authors. Contact: myasnikova@fn.csa.ru * To whom correspondence should be addressed.

We describe a data pipeline developed to extract the quantitative data on segmentation gene expression from confocal images of gene expression patterns in Drosophila. The pipeline consists of 5 steps: image segmentation, background removal, temporal characterization of an embryo, data registration and data averaging. This pipeline was successfully applied to obtain quantitative gene expression data at cellular resolution in space and at the 6.5 minute resolution in time, as well as to construct a spatiotemporal atlas of segmentation gene expression. Each data pipeline step can be easily adapted to process a wide range of images of gene expression patterns.

The segmentation gene network in Drosophila embryo solves the fundamental problem of embryonic patterning: how to establish a periodic pattern of gene expression, which determines both the positions and the identities of body segments. The gap gene network constitutes the first zygotic regulatory tier in this process. Here we have applied the systems-level approach to investigate the regulatory effect of gap gene Kruppel (Kr) on segmentation gene expression. We acquired a large dataset on the expression of gap genes in Kr null mutants and demonstrated that the expression levels of these genes are significantly reduced in the second half of cycle 14A. To explain this novel biological result we applied the gene circuit method which extracts regulatory information from spatial gene expression data. Previous attempts to use this formalism to correctly and quantitatively reproduce gap gene expression in mutants for a trunk gap gene failed, therefore here we constructed a revised model and showed that it correctly reproduces the expression patterns of gap genes in Kr null mutants. We found that the remarkable alteration of gap gene expression patterns in Kr mutants can be explained by the dynamic decrease of activating effect of Cad on a target gene and exclusion of Kr gene from the complex network of gap gene interactions, that makes it possible for other interactions, in particular, between hb and gt, to come into effect. The successful modeling of the quantitative aspects of gap gene expression in mutant for the trunk gap gene Kr is a significant achievement of this work. This result also clearly indicates that the oversimplified representation of transcriptional regulation in the previous models is one of the reasons for unsuccessful attempts of mutant simulations. Systems biology is aimed to develop an understanding of biological function or process as a system of interacting components. Here we apply the systems-level approach to understand how the blueprints for segments in the fruit fly Drosophila embryo arise. We obtain gene expression data and use the gene circuits method which allow us to reconstruct the segment determination process in the computer. To understand the system we need not only to describe it in detail, but also to comprehend what happens when certain stimuli or disruptions occur. Previous attempts to model segmentation gene expression patterns in a mutant for a trunk gap gene were unsuccessful. Here we describe the extension of the model that allows us to solve this problem in the context of Kruppel (Kr) gene. We show that remarkable alteration of gap gene expression patterns in Kr mutants can be explained by dynamic decrease of the activating effect of Cad on a target gene and exclusion of Kr from the complex network of gap gene interactions, that makes it possible for other interactions, in particular between hb and gt, to come into effect.