EDGE CMT: Genomic characterization of mammalian adaptation to frugivory

EDGE CMT：哺乳动物适应果食的基因组特征

• 批准号: 10439977
• 负责人: Nadav Ahituv
• 金额: $ 36.84万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN FRANCISCO
• 依托单位国家: 美国
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-01-14 至 2025-12-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10439977
• 关键词: ATAC-seq; Alleles; Area; Bioinformatics; Biological Assay; Candidate Disease Gene; Cell Line; Cells; ChIP-seq; Chiroptera; Collaborations; Comparative Biology; Comparative Genomic Analysis; Complex; Diabetes Mellitus; Diet; Discipline; Disease; Eating; Ecology; Educational process of instructing; Endocrine; Engineering; Environment; Ethnic group; Evolution; Fasting; Festival; Fruit; Funding; Gene Expression; Genes; Genetic; Genetic Determinism; Genetic Engineering; Genome; Genomics; Genotype; Health education; High School Student; Human; In Vitro; Insecta; Internships; Kidney; Knock-in Mouse; Laboratories; Lead; Learning; Learning Module; Liver; Mammals; Mentorship; Metabolic; Metabolic Diseases; Modeling; Molecular; Molecular Evolution; Morphology; Mus; Pancreas; Persons; Phenotype; Positioning Attribute; Primates; Proteins; RNA; Reagent; Regulator Genes; Regulatory Element; Regulatory Pathway; Reporter; Research; Resources; San Francisco; Schools; Science; Scientist; Skeletal Muscle; Small Intestines; Students; Techniques; Technology; Testing; Thick; Time; Tissues; Training; Universities; Validation; Variant; Work; base; career; cell type; comparative genomics; cost; design; diabetes risk; dietary; epigenomics; functional genomics; functional outcomes; genome analysis; human disease; improved; interest; kidney medulla; member; mouse genetics; outreach; science education; single-cell RNA sequencing; sugar; therapeutic development; trait; transcriptome sequencing; transcriptomics; undergraduate student

PROJECT SUMMARY Overview: A comprehensive molecular understanding of how mammals ascertain complex traits to adapt to specific environments remains largely unknown. Here, we will take advantage of comparative and functional genomics to systematically dissect dietary adaptation in mammals using frugivory as a model. Mammals evolved from a common dietary ancestor to have an extremely broad range of diets. Amongst these, frugivorous adaptation is of particular significance, as fruit-eating arose in multiple lineages within primate and bat orders. Frugivorous adaptation is also of general interest as diets rich in sugar increase risk for diabetes and metabolic disease in many mammals, including humans. Conversely, frugivorous primates and bats can eat large quantities of fruit/sugar without apparent disease consequences. Supported by recent advances in genome availability and genomic technologies, we plan to take a systematic approach to uncover frugivorous molecular factors by: 1) carrying out comparative genomic analyses of primates and bats to identify sequences that were specifically accelerated in frugivorous species combined with a wide-range of genomic techniques, including RNA-seq, ATAC-seq, ChIP-seq and combined single-cell RNA-seq and ATAC-seq on metabolically pertinent insect and fruit bat tissues; and 2) functionally validate frugivory-associated sequences using cell-based gene assays, massively parallel reporter assays (MPRAs) and swapping these sequences into mice. Our work will comprehensively identify the molecular components leading to frugivory and functionally characterize the genes, regulatory elements and pathways involved in this complex trait. Intellectual Merit: As bats and primates encompass broad dietary ranges, and the evolutionary distances within each order are sufficiently small, they offer ideal models for comparison within each group and between groups to analyze the genetic determinants of dietary specializations. In addition, the use of mouse genetic engineering can allow for functional validation of genetic candidates. We plan to not only identify protein changes that lead to phenotypic differences but also gene regulatory elements that have been shown to be important drivers of morphological change and the evolution of new traits. We have all the needed reagents in place to carry out this project, including necessary bat and primate genomes as well as tissues from both insectivorous and frugivorous bats, fasted and treated or untreated with fruit, and phenotypically relevant bat and primate cell lines for MPRA. Importantly, we have all the needed expertise in our lab, routinely carrying out comparative and functional genomic assays, MPRAs and mouse engineering. With our resources and proficiency, we are in the apt position to advance understanding of the complex trait that is frugivory and ultimately genotype-phenotype relationships. Broader Impacts: This research will improve genotype-phenotype predictions with regards to diet and environment and genetic factors elucidated here have the potential to assist therapeutic developments for people with metabolic diseases like diabetes. Thus, this work will have broad-ranging impacts across disciplines of comparative biology, gene expression, bioinformatics, molecular ecology, molecular evolution and human disease. We already have numerous collaborations with several scientists established from this project, which are discussed in further detail in the project description. PI Ahituv and members of his lab working on this project will contribute to the design of teaching modules from this work. This includes teaching both at UCSF in graduate courses and at San Francisco State University (SFSU) both in undergraduate and graduate courses, where PI Ahituv and his lab members have been actively involved in teaching for years. The lab has also been enthusiastically expanding outreach through the UCSF Science and Health Education Partnership (SEP), educating at local public K-12 schools and the Bay Area Science Festival and will use project materials and findings for these. The Ahituv lab has trained over 30 undergraduate students and 10 high school students, primarily from ethnic groups lacking sufficient representation in STEM. PI Ahituv will continue to offer internships for these students to learn the details of genome analysis and manipulation through this project and encourage careers across the aforementioned disciplines through inclusive mentorship.

项目摘要 概述： 对哺乳动物如何确定复杂性状以适应特定环境的全面分子理解 环境仍然是未知的。在这里，我们将利用比较基因组学和功能基因组学 以食果动物为模型，系统地剖析哺乳动物的饮食适应。哺乳动物是从 共同的饮食祖先，有一个非常广泛的饮食范围。其中，食果适应是 特别重要的是，在灵长目和蝙蝠目的多个谱系中，吃水果的现象出现了。食果实 适应也引起了人们的普遍兴趣，因为富含糖的饮食会增加患糖尿病和代谢疾病的风险， 许多哺乳动物，包括人类。相反，食果灵长类动物和蝙蝠可以吃大量的 水果/糖没有明显的疾病后果。在基因组可用性和 基因组技术，我们计划采取系统的方法来揭示食果分子因子：1） 对灵长类动物和蝙蝠进行比较基因组分析，以确定 与广泛的基因组技术相结合，包括RNA-seq， ATAC-seq、ChIP-seq和组合的单细胞RNA-seq和ATAC-seq对代谢相关昆虫和 果蝠组织;和2）使用基于细胞的基因测定功能性验证食果相关序列， 大规模平行报告基因测定（MPRA）并将这些序列交换到小鼠中。我们的工作将 全面鉴定导致食果性的分子组分，并对食果性进行功能表征， 基因、调控元件和通路参与了这一复杂的性状。 智力优势： 由于蝙蝠和灵长类动物的饮食范围很广，每一目的进化距离也很短， 它们足够小，为每组内和组间的比较提供了理想的模型， 饮食专门化的遗传决定因素。此外，使用小鼠基因工程可以允许 基因候选者的功能验证。我们计划不仅确定导致表型突变的蛋白质变化， 差异，而且基因调控元件已被证明是形态学的重要驱动因素， 变化和新特征的进化。我们已经准备好了实施这个项目所需的所有试剂， 包括必需的蝙蝠和灵长类动物基因组以及食虫蝙蝠和食果蝙蝠的组织， 禁食并用水果处理或未处理，以及MPRA的表型相关蝙蝠和灵长类动物细胞系。 重要的是，我们的实验室拥有所有需要的专业知识，定期进行比较和功能测试 基因组测定、MPRA和小鼠工程。凭借我们的资源和能力，我们在 位置，以促进复杂的性状，即食果性，并最终基因型-表型的理解 关系。 更广泛的影响： 这项研究将改善基因型-表型预测方面的饮食和环境和遗传 这里阐明的因素有可能帮助代谢性疾病患者的治疗发展。 比如糖尿病。因此，这项工作将对比较经济学的各个学科产生广泛的影响。 生物学、基因表达、生物信息学、分子生态学、分子进化和人类疾病。我们 已经与该项目建立的几位科学家进行了许多合作， 在项目说明中进一步详细讨论。PI Ahituv和他的实验室成员在这个项目上工作 将有助于从这项工作的教学模块的设计。这包括在加州大学旧金山分校的教学， 研究生课程和旧金山弗朗西斯科州立大学（SFSU）的本科和研究生课程， PI Ahituv和他的实验室成员多年来一直积极参与教学。该实验室还被 通过UCSF科学和健康教育伙伴关系（SEP）积极扩大外展， 教育在当地公立K-12学校和湾区科学节，并将使用项目材料， 这些发现。Ahituv实验室已经培训了30多名本科生和10名高中生， 主要来自在STEM中缺乏足够代表性的族裔群体。PI Ahituv将继续提供 为这些学生提供实习机会，通过该项目学习基因组分析和操作的细节， 通过包容性的指导，鼓励上述学科的职业生涯。