Scaling and regulation of gene expression in the developing fly embryo

Abstract

The early embryo of the fruit fly Drosophila melanogaster has long been a model system in which to investigate questions of how cells acquire information about their positions in developing organisms. Only in the past few years have technological developments in molecular biology, microscopy, and computing enabled the measurement of precise levels of gene expression in vivo in the developing fly embryo at the levels of single-cell protein concentrations and single sites of mRNA transcription. In this work I discuss two projects that take advantage of these recent advances in order to push the limits of our understanding, both in how cells receive precise information about position and how this information is regulated by the genes of the patterning gene network. The first of these projects uses measurements of protein concentration, both in vivo and in vitro, in order to determine whether a key maternally-supplied patterning gene is responsible for conveying all of the information that downstream genes need to scale their expression profiles with the length of the fly embryo. We find that this maternal gene does not scale with embryo length, implying the presence of additional inputs in enabling downstream genes to scale. The second of these projects uses in vivo imaging of single transcription spots in the developing embryo in order to understand how the pattern of binding sites in the regulatory region of a gene controls the level of mRNA production, given known concentrations of input protein. Contrary to hypotheses suggesting that mRNA production level is a complicated function of the strength and position of every binding site present on the DNA sequence, we find that the level of mRNA production and the domain along the length of the embryo in which high levels of mRNA are produced are both very well characterized by a linear relationship with the number of endogenous binding sites present. The results of these projects can be refined and extended by further analysis of scaling in mutant embryos and by measuring expression level in embryos in which greater perturbations have been made to sequences of protein binding sites.