How to build a gliding mammal: Using natural phenotypic variation to define the molecular regulation of tissue morphogenesis

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Genomic changes that modify developmental gene regulatory networks (GRNs) underpin both natural phenotypic variation and inherited disease states. Thus, studying natural diversity can provide profound insights into human development and the etiology of various disorders. However, most of our knowledge presently comes from a small number of traditional model species that do represent the diversity of mammalian developmental programs. Therefore, I seek to unravel the mechanisms underlying convergent evolution of major phenotypic innovations as a way to discover uncharacterized developmental programs shared among mammals. Here, I propose to define the developmental regulation of the gliding membrane or patagium, a specialized skin structure connecting the fore and hindlimbs that allows unpowered flight. Notably, the patagium has arisen independently six times among disparate mammal lineages. Because of its remarkable convergence, I hypothesize that the patagium may reflect GRNs that are shared among all mammals. Thus, the research I propose will uncover highly generalizable principles about mammalian development and will significantly expand our understanding of how conserved GRNs are re-deployed to generate phenotypic novelty. My proposal consists of three aims that together present an exciting roadmap to address this fundamental question. In Aim 1, I will profile the transcriptional landscape of the patagium in the sugar glider (Petaurus breviceps) and compare it to that of adjacent skin and to lateral skin in a non-gliding marsupial, the fat-tailed dunnart (Sminthopsis crassicaudata) and in the laboratory mouse. I will use gene network analyses to identify regulatory modules with patagium-specific activities and within them, genes that are differentially expressed in the patagium. In Aim 2, I will define intramodular regulatory relationships using an upregulation- qPCR screen. I will then test the necessity and sufficiency of identified regulatory genes to drive patagium phenotypes through in vivo experiments in the glider, dunnart and mouse. This comparative approach will allow me to distinguish conserved mammalian developmental programs from novel programs in gliders. In parallel with Aims 1 and 2, I will define the cis-regulatory circuitry controlling patagium gene expression in Aim 3. I will use epigenomic profiling to locate active enhancers of patagium genes and analysis of evolutionary rates to identify enhancers evolving adaptively in gliders. The loci that emerge from these independent, but complementary approaches will then be functionally investigated using STARR-Seq. Uncovering developmental program of the patagium will provide a framework for how gene regulatory information is translated into morphological outputs and how conserved developmental programs are re-deployed to drive novel phenotypes. Under the supervision of my co-sponsors, I will accomplish three major training objectives: 1) gaining experience in functional genomics, 2) learning techniques in molecular and developmental biology and 3) building career skills that will be necessary as I move toward greater independence as a researcher.