Lighting Up the Central Dogma in Embryonic Development

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Our understanding of biological phenomena is often shaped by the technology available to query our system of interest. For years, our understanding of embryonic development has been dictated by static snapshots stemming from technologies that rely on the examination of dead, fixed embryos. In this case, the spatiotemporal evolution of the gene expression programs that shape animal body plans is inferred from static images. The main hypothesis of the proposed work is that the reliance on snapshots rather than movies has hidden deep insights from view relevant to embryonic development. We propose to break free from the reign of static snapshots in the study of developmental biology by introducing new technologies that will make it possible to redo the subject of embryonic development from the standpoint of dynamics through the imaging and quantification of the central dogma in real time at the single cell level within living embryos. We will use the embryonic development of the fruit fly Drosophila melanogaster as a proof of principle in order to (i) develop new technology to quantify fast changing transcription factor concentrations and the resulting transcriptional output in development, (ii) develop new in vivo fluorescent probes to augment cutting-edge lattice light-sheet microscopy to make it possible to directly visualize how single activators and repressors bind to the DNA, and (iii) combine these input-output measurements with our single-molecule measurements in order to directly visualize the molecular mechanisms by which transcription factors perform their regulatory function in real time in living embryos. We argue that only by enabling this real-time description of gene regulatory programs in development can we reach a quantitative understanding that makes it possible to predict how DNA sequence dictates cellular commitment and how, when this regulation goes awry, developmental defects and states of unchecked cellular proliferation ensue.