Pattern formation by dynamically interacting network motifs.

Systematic validation of pattern formation mechanisms revealed by molecular studies of development is essentially impossible without mathematical models. Models can provide a compact summary of a large number of experiments that led to mechanism formulation and guide future studies of pattern formation. Here, we realize this program by analyzing a mathematical model of epithelial patterning by the highly conserved EGFR and BMP signaling pathways in Drosophila oogenesis. The model accounts for the dynamic interaction of the feedforward and feedback network motifs that control the expression of Broad, a zinc finger transcription factor expressed in the cells that form the upper part of the respiratory eggshell appendages. Based on the combination of computational analysis and genetic experiments, we show that the model accounts for the key features of wild-type pattern formation, correctly predicts patterning defects in multiple mutants, and guides the identification of additional regulatory links in a complex pattern formation mechanism.

A combinatorial code for pattern formation in Drosophila oogenesis.

Two-dimensional patterning of the follicular epithelium in Drosophila oogenesis is required for the formation of three-dimensional eggshell structures. Our analysis of a large number of published gene expression patterns in the follicle cells suggests that they follow a simple combinatorial code based on six spatial building blocks and the operations of union, difference, intersection, and addition. The building blocks are related to the distribution of inductive signals, provided by the highly conserved epidermal growth factor receptor and bone morphogenetic protein signaling pathways. We demonstrate the validity of the code by testing it against a set of patterns obtained in a large-scale transcriptional profiling experiment. Using the proposed code, we distinguish 36 distinct patterns for 81 genes expressed in the follicular epithelium and characterize their joint dynamics over four stages of oogenesis. The proposed combinatorial framework allows systematic analysis of the diversity and dynamics of two-dimensional transcriptional patterns and guides future studies of gene regulation.

Spatial regulation of BMP signaling by patterned receptor expression.

Local delivery of TGF-beta/BMP ligands is commonly used as a tissue engineering strategy for the spatial regulation of cell growth and differentiation. While the location and the dose of ligand are the only parameters that influence the spatial distribution and biological effects of the ligand in vitro, in vivo genetic studies of development reveal that spatial control of TGF-beta/BMP signaling can be accomplished at multiple levels, from ligand release to signal interpretation. Here we focus on spatial control of BMP signaling by patterned receptor expression. Motivated by our recent experimental analysis of the two-dimensional BMP signaling patterns in the developing Drosophila egg, we formulate one- and two-dimensional models of ligand diffusion and internalization in the presence of patterned receptor expression. Our analysis of these models shows that they can capture the quantitative features of the experimentally observed pattern of phosphorylated SMAD in Drosophila oogenesis and shows that patterned receptor expression provides versatile control of BMP signaling in developing tissues. Quantitative understanding of the mechanisms of spatiotemporal control of signaling pathways in development is essential for successful harnessing of these pathways in tissue engineering.

Drosophila eggshell is patterned by sequential action of feedforward and feedback loops.

During Drosophila oogenesis, patterning activities of the EGFR and Dpp pathways specify several subpopulations of the follicle cells that give rise to dorsal eggshell structures. The roof of dorsal eggshell appendages is formed by the follicle cells that express Broad (Br), a zinc-finger transcription factor regulated by both pathways. EGFR induces Br in the dorsal follicle cells. This inductive signal is overridden in the dorsal midline cells, which are exposed to high levels of EGFR activation, and in the anterior cells, by Dpp signaling. We show that the resulting changes in the Br pattern affect the expression of Dpp receptor thickveins (tkv), which is essential for Dpp signaling. By controlling tkv, Br controls Dpp signaling in late stages of oogenesis and, as a result, regulates its own repression in a negative-feedback loop. We synthesize these observations into a model, whereby the dynamics of Br expression are driven by the sequential action of feedforward and feedback loops. The feedforward loop controls the spatial pattern of Br expression, while the feedback loop modulates this pattern in time. This mechanism demonstrates how complex patterns of gene expression can emerge from simple inputs, through the interaction of regulatory network motifs.