In developmental biology, a morphogen is any molecule that acts at different concentrations to cause cells to do different things. In many animal embryos, concentration gradients of morphogens allow cells to decide where they are in the body and how they should behave. Morphogens often have such a function by binding to regulatory DNA switches (or DNA sequences) that can turn on specific genes, which in turn influence cell behavior. Many areas of biological investigation would be advanced significantly if it was understood how regulatory DNA sequences encode these concentration-threshold specific responses. The reason is that all regulatory DNA switches, not just those that respond to morphogens, need to encode concentration-thresholds. In this project, a large set of regulatory DNA switches will be examined that respond to the same morphogen, specifically a protein called Dorsal that patterns one of the embryonic body axes (the dorsal-ventral axis) in the fruit fly. In this research study, DNA sequences that read out different concentrations of the Dorsal protein will be compared and manipulated in an effort to break the code for this classical morphogen system. In addition, new students will be trained in cutting edge genomics and molecular biology and will identify new principles in how cells regulate gene expression. These principles are expected to apply broadly to other tissues and other organisms (including humans) because the system being studied uses basic components that are widely conserved.
Our study has resulted in a better understanding of the regulatory DNA sequences that help pattern animal embryos during development. Among the several discoveries associated with this project, one in particular is important for understanding the need for multiplexing developmental signals during animal development, and it has to do with something as basic as space and time. We identified the need to integrate two different morphogen gradient signals at a developmental enhancer DNA in order to resolve conflicting spatiotemporal constraints. Enhancers targeted by morphogen signaling may drive temporally inappropriate expression because morphogen gradients also provide temporal cues (i.e., a morphogenic gradient is developmentally dynamic, building up and then decaying in peak amplitude). Thus, a high-threshold response selected for its role in driving a spatially restricted expression pattern may be inappropriate when an early, optimal temporal expression pattern demands a low-threshold response. Using the powerful neurogenic ectoderm enhancer (NEE) system of Drosophila, we articulate and address the spatiotemporal conflict problem inherent to morphogenic response encoding. In this study, we identify spatiotemporal conflict in the NEE-driven regulation of the gene ventral neurons defective (vnd), which must be precisely regulated for proper dorsal/ventral patterning of the nervous system. In particular, vnd plays a critical role in specifying distinct D/V neural columnar fates of the ectodermal compartments by encoding a repressor of more dorsal regulators. The role of vnd in this regulatory hierarchy requires early temporal expression, which is characteristic of low-threshold responses, but its specification of ventral neurogenic ectoderm demands a relatively high-threshold response to the morphogen. The study shows that the NEE at vnd takes additional input from the complementary gradient of the Dpp morphogen via a highly conserved Schnurri/Mad/Medea Silencer Element (SMMSE), which is integral to its NEE module. Hence, at least two morphogen gradients along the the same axis but shifted slightly in temporal onsets and offsets will usually be required in order to produce different spatial readouts without also scrambling their temporal onsets and offsets inappropriately. Other outcomes from this project are just as important and will allow a better understanding of the functions of regulatory DNA elements in animal genomes.
