Three-dimensional morphology and gene expression mapping for the Drosophila blastoderm

To properly understand the transcriptional network of animals, we must have full quantitative comprehension of the spatial and temporal expression patterns of transcription factors and their targets. Visual inspection of embryos stained to reveal the patterns of genes shows levels of expression that change from cell to cell in a complex manner. With our current wealth of knowledge regarding the basic biology of animal genomes and the components of their transcriptional regulatory networks, combined with current technologies in optical microscopy, computing, and image and vision analysis, we should be able to capture quantitative, three-dimensional (3D) information about the transcriptional network (all factors and targets) for an entire animal at cellular resolution. It should also be possible to assemble these data into a single computationally analyzable database--an atlas--that could be the basis for uncovering new biology governing regulatory gene networks. This article describes progress toward realizing these goals, with the focus on Drosophila melanogaster. It describes a suite of high-throughput methods that have been used to create the first quantitative 3D description of gene expression and morphology at cellular resolution in a whole animal, and it presents some of the new biology that has been revealed by this quantitative atlas.