Using Minimal Synthetic Enhancers to Reach a Predictive Understanding of Transcriptional Regulation in Development

Abstract

In the past few decades, developmental biologists have made tremendous progress identifying enhancers and binding motifs for transcription factors that drive the expression of genes responsible for cell fate decisions. Despite this progress, we are still incapable of determining mRNA transcript copy numbers given a regulatory DNA architecture and transcription factor concentrations. Recently, several genetic and microscopy tools have been developed that make it possible to engage in such dialogue between theory and experiment in the context of living embryos of the fruit fly Drosophila melanogaster. We use thermodynamic models to predict how the placement, number, and affinity of binding sites for transcription factors govern transcriptional dynamics in the embryo. To experimentally test the predictions stemming from these models, we designed a minimal gene cassette that serves as a scaffold for systematically modulating regulatory parameters. Our gene construct includes MS2 bacteriophage stem loop sequences to report on gene expression from an enhancer with one or more copies of the Bicoid activator and Zelda co-activator binding motifs. Our experiments show that the number and affinity of binding motifs modulate the probability that nuclei initiate transcription and their rate of polymerase recruitment in a manner consistent with equilibrium thermodynamic models.