Discovery and analysis of the C. elegans neuronal gene expression network (CENGEN)

线虫神经元基因表达网络 (CENGEN) 的发现和分析

• 批准号: 9473492
• 负责人: MARC HAMMARLUND
• 金额: $ 111.28万
• 依托单位: YALE UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2017
• 资助国家: 美国
• 起止时间: 2017-09-25 至 2022-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9473492
• 关键词: Address; Adult; Affect; Age; Alternative Splicing; Anatomy; Animals; Area; Behavioral; Biological; Brain; Caenorhabditis elegans; Catalogs; Cell Lineage; Cells; Code; Communities; Complex; Data; Data Set; Development; Dimensions; Disease; Disease susceptibility; Dissociation; Fluorescence; Future; Gene Expression; Gene Expression Profile; Gene Expression Regulation; Genes; Genetic; Genome; Goals; Individual; Injury; Knowledge; Label; Link; Logic; Maps; Mediating; Methods; MicroRNAs; Molecular; Molecular Profiling; Natural regeneration; Nervous system structure; Neurons; Neurosciences; Neurotransmitters; Organism; Outcome; Pathology; Pathway Analysis; Pattern; Physiology; Process; Proteins; Public Health; RNA; RNA Splicing; Recovery; Regulation; Reporter; Reporter Genes; Reproducibility; Research; Resolution; Resources; Sampling; Sorting - Cell Movement; Specificity; Structure; System; Techniques; Technology; Tissue-Specific Gene Expression; Transcript; Transgenic Organisms; Untranslated RNA; behavior influence; cost; deep sequencing; differential expression; gene function; genome editing; innovation; insight; intersectionality; mRNA Expression; male; mature animal; neurogenetics; novel; overexpression; promoter; protein profiling; sequencing platform; sex; single cell sequencing; transcriptome; transcriptome sequencing; young adult

PROJECT SUMMARY There is a current lack of understanding of differential gene expression within the nervous system. Ideally one would like to know, across all neuron types, exactly how the genome is transcribed and processed into functional RNAs. This information is fundamentally important because differential gene expression defines the form and function of individual neurons, determines how individual neurons contribute to circuit physiology and behavior, and influences how individual neurons are affected by injury and disease. Further, detailed and complete knowledge of differential gene expression within the nervous system would help elucidate the logic and cellular mechanisms that generate neuronal diversity, including regulation of gene expression, alternative splicing, and miRNA function. Yet progress in this area has been limited: For most nervous systems, the exact number of distinct types of neurons is unknown and therefore a global map of neuron-specific gene expression is not achievable. Here we propose to address this problem in a project to discover and analyze the C. elegans Neuronal Gene Expression Map & Network (CeNGEN). The C. elegans nervous system contains precisely 302 total neurons comprising 118 classes of distinct neuronal types. We propose to exploit this unique attribute to analyze gene expression with high accuracy in every individual neuronal type. CeNGEN proceeds in four specific aims. Aim 1) Establish 118 transgenic strains, each one expressing fluorescent markers that uniquely label a single type of neuron. Aim 2) Use innovative cell dissociation and FACS methods to isolate each type of neuron from age-matched adults, and use RNA-seq approaches to assess global coding transcript and miRNA expression, as well as splicing diversity. Aim 3) Utilize single cell sequencing technology to precisely map gene expression over multiple parameter spaces. Aim 4) Build cell-centered and gene-centered expression maps, and seek connections with other uniquely known features of the C. elegans nervous system including the wiring diagram, the cell lineage, neurotransmitter identity, and function. CeNGEN represents a paradigmatic advance in neurogenetics, and provides a unique opportunity to elucidate the global control of neuron-specific gene expression and to relate gene expression to neuronal wiring and function. Expected significant outcomes include: Identification of conserved regulatory mechanisms that generate neuronal specificity and diversity; Detailed understanding of alternative splicing and miRNA function across the nervous system; Relationship of differential gene expression to neuronal lineage, anatomy, function and connectivity. CeNGEN will also serve as a resource for future studies in C. elegans neuroscience, and will provide a framework for addressing global differential gene expression in more complex nervous systems that are currently not amenable to this comprehensive approach.

项目摘要 目前缺乏对神经系统中差异基因表达的了解。理想情况下一个 想知道，在所有神经元类型中，确切地将基因组转录和处理到 功能性RNA。该信息在根本上很重要，因为差异基因表达定义了 单个神经元的形式和功能确定单个神经元如何促进电路生理和 行为，并影响单个神经元受伤和疾病的影响。此外，详细 完全了解神经系统中差异基因表达将有助于阐明逻辑 以及产生神经元多样性的细胞机制，包括调节基因表达，替代 剪接和miRNA功能。然而，该领域的进展受到限制：对于大多数神经系统，确切的 不同类型的神经元的数量是未知的，因此是神经元特异性基因表达的全局图 无法实现。在这里，我们建议在发现和分析秀丽隐杆线虫的项目中解决这个问题 神经元基因表达图和网络（Cengen）。秀丽隐杆线虫神经系统精确包含302 总神经元包括118类不同的神经元类型。我们建议将这种独特属性利用为 在每种单独的神经元类型中以高精度分析基因表达。彭根（Cengen）四分之一 具体目标。目标1）建立118个转基因菌株，每个菌株都表达荧光标记物 标记一种类型的神经元。目标2）使用创新的细胞解离和FACS方法隔离每种类型的 年龄匹配的成年人的神经元，并使用RNA-Seq方法评估全局编码本和miRNA 表达以及剪接多样性。目标3）利用单细胞测序技术精确映射基因 在多个参数空间上表达。目标4）建立以细胞为中心的和以基因为中心的表达图， 并寻求与秀丽隐杆线虫神经系统的其他独特特征的联系 接线图，细胞谱系，神经递质的身份和功能。 Cengen代表范式 在神经遗传学方面发展，并提供了一个独特的机会来阐明神经元特异性的全球控制 基因表达并将基因表达与神经元接线和功能相关联。预期的重大结果 包括：识别产生神经元特异性和多样性的保守调节机制； 详细了解整个神经系统中的替代剪接和miRNA功能；关系 差异基因表达对神经元谱系，解剖学，功能和连通性。 Cengen也将服务 作为秀丽隐杆线虫神经科学的未来研究的资源，将为解决全球提供一个框架 目前不适合此的更复杂的神经系统中的差异基因表达 全面的方法。