Title: Interrogating gene regulatory circuit function using natural variation in animals

Abstract: The long-term goal of my work is to understand how regulatory information is encoded in animal genomes using high-resolution imaging, genetics, computational models and bioinformatics. Regulatory DNA, e.g. enhancers, can be thought of as the “wiring diagram” for a transcriptional circuit, whose output is gene expression and whose inputs are regulatory molecules like transcription factors (TFs). Because enhancers change rapidly in sequence over even short evolutionary time, examining the expression patterns driven orthologous enhancers can elucidate the rules governing the sequence-function relationship of enhancers. However, multiple components of transcriptional circuits change during evolution, so changes in gene expression output can be caused by either changes in the circuit’s inputs or changes in the circuit wiring. Even when an expression pattern is conserved between species, the regulatory DNA and TFs can be functionally divergent, yet work together to produce a similar expression pattern of their target gene. Therefore, to understand sequence-function relationships of regulatory DNA, we must first control for gene expression divergence due to changing inputs.

Using transcriptional circuits in the anterior-posterior patterning network in Drosophila blastoderm stage embryos, we have developed a modeling framework for disentangling the contributions of changes in enhancers and changes in the expression pattern of their TF inputs. Using cellular-resolution imaging techniques, we created atlases of gene expression for key TFs in the anterior-posterior patterning network in several Drosophila species. We use these data and modeling framework to compare the function of two transcriptional circuits in the embryo that show differing patterns of conservation. We expect to generalize this approach to other types of regulatory DNA and transcriptional circuits in other systems to understand how sequence divergence affects regulatory function and its implications for the evolution of gene regulation.