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

改变发育基因调控网络（GRNs）的基因组变化支持了自然和非自然的基因表达。 表型变异和遗传疾病状态。因此，研究自然多样性可以提供深刻的 对人类发展和各种疾病的病因学的见解。然而，我们的大部分知识 目前来自少数传统的模式物种，代表了哺乳动物的多样性， 发展方案。因此，我试图解开趋同进化的机制， 主要的表型创新作为一种方法来发现未表征的发展程序之间共享 哺乳动物在这里，我建议定义滑行膜或翼膜的发育调节， 连接前肢和后肢的特殊皮肤结构，允许无动力飞行。特别是 翼膜在不同的哺乳动物谱系中独立出现了六次。因其显著 收敛，我假设，翼膜可能反映GRNs之间共享的所有哺乳动物。因此，在本发明中， 我所建议研究将揭示哺乳动物发育的高度普遍性原则， 显著扩展了我们对保守GRNs如何重新部署以产生表型 新奇我的建议包括三个目标，共同提出了一个令人兴奋的路线图来解决这个问题 根本问题。在目标1中，我将描绘糖滑翔机中翼膜的转录景观 （Petaurus breviceps），并将其与非滑行有袋动物的相邻皮肤和侧皮肤进行比较， 在实验室小鼠中，我会用基因网络分析 鉴定具有翼膜特异性活性的调控模块，以及在其中，差异表达的基因， 在翼膜中表达。在目标2中，我将使用上调来定义模块内调节关系- qPCR筛选。然后，我将测试必要性和充分性，已确定的调控基因，以驱动翼膜 通过在滑翔机，邓纳特和小鼠体内实验的表型。这种比较方法将 请允许我区分哺乳动物的保守发育程序和滑翔机的新程序。在 与目标1和2平行，我将定义控制Aim中翼膜基因表达的顺式调节回路 3.我将使用表观基因组分析来定位patagium基因的活性增强子，并分析其进化过程。 速率来识别滑翔机中自适应进化的增强器。从这些独立的，但 然后将使用STARR-Seq对互补方法进行功能研究。揭开 发育程序的翼膜将提供一个框架，基因调控信息是如何 转化为形态输出，以及如何重新部署保守的发展计划， 新的表型在我的共同赞助商的监督下，我将完成三个主要的培训目标： 1)获得功能基因组学的经验，2）学习分子和发育生物学的技术 3）培养职业技能，这对我作为一名研究人员走向更大的独立性是必要的。

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.