EDGE CMT: Genomic characterization of mammalian adaptation to frugivory

项目总结 概述： 对哺乳动物如何确定复杂特征以适应特定特征的全面分子理解 环境在很大程度上仍然是未知的。在这里，我们将利用比较基因组学和功能基因组学 以果树为模型，系统地剖析哺乳动物的饮食适应。哺乳动物是从一个 共同的饮食祖先拥有极其广泛的饮食范围。其中，食果性适应是 特别重要的是，因为吃水果在灵长类和蝙蝠目中出现了多个谱系。食果性 适应也是普遍感兴趣的，因为富含糖的饮食增加了患糖尿病和代谢性疾病的风险。 许多哺乳动物，包括人类。相反，食果的灵长类动物和蝙蝠可以摄取大量的 水果/糖，没有明显的疾病后果。由基因组可获得性和最新进展支持 基因组技术，我们计划采取一种系统的方法来揭示食果性分子因子，具体如下：1) 对灵长类和蝙蝠进行比较基因组分析，以确定特定的序列 在食果性物种中加速结合广泛的基因组技术，包括RNA-seq， ATAC-SEQ、CHIP-SEQ及联合单细胞RNA-SEQ和ATAC-SEQ对代谢相关昆虫的作用 果蝠组织；以及2)使用基于细胞的基因分析在功能上验证与果树相关的序列， 大规模平行报告分析(MPRA)，并将这些序列交换到小鼠中。我们的工作将 全面鉴定导致果实的分子成分，并从功能上表征 参与这一复杂特征的基因、调控元件和途径。 智力价值： 因为蝙蝠和灵长类动物的饮食范围很广，每个目之间的进化距离是 足够小，它们提供了理想的模型，用于在每个组内和组之间进行比较，以分析 饮食专业化的遗传决定因素。此外，使用老鼠基因工程可以允许 基因候选的功能验证。我们计划不仅识别导致表型的蛋白质变化 差异，但也是基因调控元件，已被证明是形态的重要驱动因素 新特征的变化和进化。我们已经准备好了执行这个项目所需的所有试剂， 包括必要的蝙蝠和灵长类基因组以及食虫和食果蝙蝠的组织， 禁食和水果处理或不处理，以及与MPRA表型相关的蝙蝠和灵长类细胞系。 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 基因组分析、MPRAs和小鼠工程。凭借我们的资源和熟练程度，我们是在APT 促进对果树的复杂性状以及最终的基因-表型的理解 两性关系。 更广泛的影响： 这项研究将改进关于饮食、环境和遗传的基因型-表型预测。 在此阐明的因素有可能有助于新陈代谢患者的治疗进展 像糖尿病这样的疾病。因此，这项工作将对比较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大量合作，这些科学家包括 在项目说明中进行了更详细的讨论。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中设计教学模块。这包括在加州大学旧金山分校任教 研究生课程和旧金山州立大学(SFSU)的本科和研究生课程， 多年来，Pi Ahituv和他的实验室成员一直积极参与教学工作。实验室也一直在 积极通过加州大学旧金山分校的科学和健康教育伙伴关系(SEP)扩大宣传范围， 在当地公立K-12学校和湾区科学节进行教育，并将使用项目材料和 关于这些的发现。阿希图夫实验室已经培养了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，通过这个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发展。

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.