A unifying feature of an organism's appearance (or "phenotype") is its construction during the events of development. Each phenotypic trait requires the cooperation of a collection of genes whose participation is controlled by DNA sequences known as cis-regulatory elements (CREs). CREs work like switches to turn genes ON or OFF in certain cell types at specific life stages. The switch-like function of CREs are encoded in the DNA sequence by short stretches of ordered bases to which proteins known as transcription factors specifically bind. Combinations of transcription factors form a "logic" of instructions that determines precisely which cells, and at what time the CRE can switch a gene ON. Currently, it remains poorly understood how switch-like functions are encoded in CREs and how traits evolve through changes in their encoded logic. In particular, the Hox transcription factors represent a poorly understood class that provides CREs with positional information along the major body axis. The Williams and Rebeiz labs are collaborating to study the network of genes and CREs responsible for making a male-specific body pigmentation of the fruit fly species Drosophila melanogaster. The results will inform how such pigmentation originated and was altered in multiple lineages of fruit fly species. The outcomes will show how the construction of a new characteristic is controlled by Hox genes, CREs and how evolution can operate at the level of binding sites for transcription factors. This work will provide a picture of trait evolution that will be applicable to a wide variety of animal systems. Through this research, computational tools will be refined and online learning resources will be created to aid scientists. This research project will support the future of science personnel through the participation of high school students, undergraduate students, and graduate students in mentored research. Participation will emphasize students from under-represented groups in science.
The developmental events that pattern the animal body plan are regarded as a crucible for the evolution of novel traits. This project's overarching goal is to understand how body plan patterning information originated in a gene regulatory network (GRN), and was subsequently modified to diversify a morphological trait. GRNs are structured to pattern development through the binding of transcription factors to cis-regulatory elements (CREs) to control gene expression. The combination of factors that bind CREs form a regulatory logic that specifies timing, pattern and levels of expression. Currently, very little is known about how GRN structure evolves to generate different phenotypes. Specifically, which genes in the hierarchy were modified, and ultimately how regulatory logic evolves. The Williams and Rebeiz labs are examining the evolution of a GRN and its underlying regulatory logic for a rapidly evolving trait present in an experimentally tractable animal system. The proposed studies will focus on male-specific patterns of abdominal pigmentation that convergently evolved in two fruit fly lineages, which were then modified and lost. The first aim will characterize how the arbiters of the body plan (e.g. Hox proteins, cofactors, and activity modulators) directly interact with CREs of the GRN to control expression patterns of pigmentation enzymes in D. melanogaster. The second aim will determine how this Hox-regulated GRN was altered in cases where pigmentation was expanded, contracted, or lost in non-model fruit fly species. The third aim will trace how this GRN independently evolved a convergent pigmentation phenotype in a non-model fly. To pursue these aims, the research team will employ techniques that include reporter transgenes in multiple fruit fly species and gel shift assays between transcription factors and CRE sequences to pinpoint phenotype altering mutations and connect these to the alterations in transcription factor binding and function that they inspired.
