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

如何构建滑翔哺乳动物：利用自然表型变异来定义组织形态发生的分子调控

基本信息

批准号：
10517079
负责人：
Charles Yakov Feigin
金额：
$ 3.49万
依托单位：
PRINCETON UNIVERSITY
依托单位国家：
美国
项目类别：
财政年份：
2020
资助国家：
美国
起止时间：
2020-12-01 至 2022-05-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/10517079
关键词：
Address Animal Experimentation Animals Antibodies Biological Assay Candidate Disease Gene ChIP-seq Communication Research Data Analyses Development Developmental Biology Developmental Gene Disease Doctor of Philosophy Enhancers Etiology Evolution Faculty Fatty acid glycerol esters Forelimb Gene Expression Gene Expression Profile Genes Genetic Genome Genomics Genotype Health Hereditary Disease Hindlimb Home House mice Human Human Development Individual Knowledge Laboratory mice Lateral Learning Mammals Marsupialia Mediating Membrane Modeling Molecular Molecular Biology Morphogenesis Morphology Mus Natural Selections Oligonucleotides Orthologous Gene Outcome Output Pathway Analysis Phenotype Professional Competence Publishing Recombinant Proteins Recurrence Regulation Regulator Genes Regulatory Element Research Research Ethics Research Personnel Resources Science Scientist Skin Skin Tissue Stretching Structure Supervision Tail Techniques Testing Time Tissues Training Translating Universities Up-Regulation Variant Virus Activation base career development comparative comparative genomics design differential expression epigenomics experience experimental study functional genomics gene network gene regulatory network hands on instruction implantation improved improved outcome in vivo innovation insight interest knock-down novel overexpression post-doctoral training programs skills small hairpin RNA small molecule sugar

项目摘要

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.

改变发育基因调控网络(GRN)的基因组变化支撑着自然的表型变异和遗传性疾病状态。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的洞察。然而，我们大部分的知识目前来自少数代表哺乳动物多样性的传统模式物种发展计划。因此，我试图解开收敛进化背后的机制重大表型创新，作为发现共同的未定性发展计划的一种方式哺乳动物。在这里，我建议定义滑膜或穹隆的发育调节，a 连接前肢和后肢的特殊皮肤结构，允许无动力飞行。值得注意的是，在不同的哺乳动物谱系中，Patagium已经独立出现了六次。因为它的非凡之处收敛，我假设帕塔基团可能反映了所有哺乳动物共有的GRN。因此，我提议的研究将揭示关于哺乳动物发育的高度概括的原则，并将显著扩展我们对如何重新部署保守的GRN以生成表型的理解新奇。我的建议包括三个目标，它们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，我将描述糖滑翔机中Patagium的转录图景 (Petaurus Brevicep)，并将其与邻近皮肤和非滑行有袋类动物的侧皮进行比较，大尾袋鼠和实验室小白鼠。我将使用基因网络分析来识别具有Patagium特异性活性的调控模块及其内部的差异基因在帕塔格中表现出来。在目标2中，我将使用上调来定义模块内监管关系- QPCR筛查。然后，我将测试已识别的调控基因是否有必要和足够的能力来驱动帕塔金。通过在滑翔机、飞镖和小鼠体内的实验进行表型分析。这种比较方法将请允许我将保守的哺乳动物发育计划与滑翔机的新计划区分开来。在……里面与目标1和目标2平行，我将在目标中定义控制patagium基因表达的顺式调控电路。 3.我将利用表观基因组图谱来定位Patagium基因的活性增强子并进行进化分析在滑翔机中识别自适应进化的增强剂的速率。从这些独立的、但然后，将使用STARR-SEQ从功能上研究补充方法。揭开面纱专利的开发计划将为基因调控信息是如何提供一个框架转化为形态输出，以及如何重新部署保守的发展计划以推动新奇的表型。在我的共同赞助人的监督下，我将完成三个主要的培训目标： 1)获得功能基因组学经验；2)学习分子生物学和发育生物学技术 3)培养职业技能，这将是我作为一名研究人员走向更独立的过程中所必需的。