Genetic and genomic tools for C. briggsae research

用于 C. briggsae 研究的遗传和基因组工具

• 批准号: 10582658
• 负责人: Erik Christian Andersen
• 金额: $ 18.84万
• 依托单位: OHIO STATE UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-03-15 至 2025-02-28
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10582658
• 关键词: Address; Aging; Alleles; Apoptosis; Bacteria; Biological; Biological Process; C. elegans genome; CRISPR/Cas technology; Caenorhabditis; Caenorhabditis elegans; Cell Death; Chromosome inversion; Chromosomes; Clustered Regularly Interspaced Short Palindromic Repeats; Collection; Communities; Comparative Study; Complement; Complex; Conserved Sequence; DNA; DNA Sequence; Data; Databases; Development; Disease; Dose; Engineering; Evaluation; Evolution; Experimental Genetics; Generations; Genes; Genetic; Genetic Crossing Over; Genetic study; Genome; Genomics; Genotype; Health; Heterozygote; Hi-C; High School Student; Human; Inbreeding; Insecta; Label; Laboratories; Life; Location; Maintenance; Manuals; Maps; Mediating; Messenger RNA; Methods; MicroRNAs; Microscopic; Modeling; Mutation; Nematoda; Organism; Pathway interactions; Phenotype; Polygenic Traits; Population Biology; Population Distributions; Process; RNA Interference; RNA Probes; Reagent; Recombinants; Reproducibility; Research; Research Personnel; Research Project Summaries; Resource Development; Resources; Role; Site; Sterility; Techniques; Technology; Testing; Transgenes; Transgenic Organisms; Update; Validation; Virus; WormBase; biological systems; comparative; comparative genomics; effectiveness validation; experience; experimental study; flexibility; gene function; genetic analysis; genetic resource; genome resource; genome-wide; genomic data; genomic locus; genomic tools; improved; in vivo; interest; life history; mutant; nanopore; pathogen; prevent; reagent testing; reference genome; repaired; response; telomere; tool; tool development; trait; undergraduate student

Genetic and Genomic tools for C. briggsae research: Project Summary Research using the microscopic nematode Caenorhabditis elegans has produced many foundational discoveries in the genetic basis of cell death, organismal aging, the biological roles for microRNAs, as well as other fundamental topics that are relevant to human health. An important complement to studies on C. elegans is those on the related nematode Caenorhabditis briggsae, which shares many of the experimental strengths of C. elegans, but from which it diverged approximately 30 million years ago. C. briggsae provides a platform for comparative genetic studies, leading to efficient analysis of conserved processes, as well as discoveries on the evolution of genes, pathways and networks. These comparative studies are important in establishing research rigor and validating findings. In addition, differences between C. elegans and C. briggsae in terms of life history traits and global distribution of populations means that many studies addressing population biology questions, polygenic traits, or host-pathogen, commensal, and opportunistic relationships with viruses, bacteria, and insects are better done with C. briggsae than with C. elegans. Despite these important features, many genetic resources that are essential for standard C. elegans research are not available for studies using C. briggsae. With the increasing efficiency of genetic editing and engineering using CRISPR-mediated methods, the availability of important genomic and genetic tools is a key limitation for these important comparative studies. This project will produce these research resources to address this gap. As a first aim, two telomere-to- telomere C. briggsae reference genomes with validated gene models will be produced, using sets of complementary long and short sequence read methods and validation techniques. These data will be incorporated into NCBI and Wormbase, the online database used by researchers who use C. elegans and related nematodes. A second aim will produce and validate a set of genetic balancers, or rearranged chromosomes that prevent meiotic crossing over. These genetic tools are critical for the maintenance and evaluation of mutations that are homozygous lethal or sterile and that are currently maintained through laborious processes. Genetic balancers will also permit more complex genetic experiments not currently feasible in C. briggsae. Finally, strains with "safe harbor" landing sites for the introduction of DNA into defined locations in the C. briggsae genome will be produced and validated. These strains will permit controlled, reproducible introduction of single copy insertion clones into C. briggsae, and permit a range of experimental manipulation including gene "node swaps" between the two species, and the testing of reagents developed for C. elegans directly in C. briggsae. Together, these aims will produce key tools that remove important barriers to genetic analysis in this research organism.

用于 C. briggsae 研究的遗传和基因组工具：项目摘要 使用显微线虫秀丽隐杆线虫的研究已经产生了许多基础性成果 在细胞死亡的遗传基础、有机体衰老、microRNA 的生物学作用以及 与人类健康相关的其他基本主题。对 C 研究的重要补充。 线虫是相关线虫 Caenorhabditis briggsae 上的线虫，它与许多实验结果相同 线虫的优势，但它在大约 3000 万年前就与线虫发生了分歧。 C. briggsae 提供了 比较遗传学研究平台，可有效分析保守过程，以及 关于基因、途径和网络进化的发现。这些比较研究很重要 建立研究的严谨性并验证研究结果。此外，秀丽隐杆线虫和 C. elegans 之间的差异。 briggsae 在生活史特征和全球人口分布方面意味着许多研究涉及 群体生物学问题、多基因性状或宿主-病原体、共生和机会主义关系 对于病毒、细菌和昆虫，用 C. briggsae 比用 C. elegans 效果更好。尽管有这些 重要特征，但许多对于标准秀丽隐杆线虫研究至关重要的遗传资源却没有 可用于使用 C. briggsae 的研究。随着基因编辑和工程利用效率的不断提高 CRISPR 介导的方法、重要基因组和遗传工具的可用性是这些方法的关键限制 重要的比较研究。 该项目将产生这些研究资源来弥补这一差距。作为第一个目标，两个端粒到 将使用一组经过验证的基因模型来生成端粒 C. briggsae 参考基因组 互补的长和短序列读取方法和验证技术。这些数据将 纳入 NCBI 和 Wormbase，这是使用线虫的研究人员使用的在线数据库 相关线虫。第二个目标是产生并验证一组基因平衡器，或重新排列 阻止减数分裂交叉的染色体。这些遗传工具对于维持和 评估纯合致死或不育突变，并且目前通过 费力的过程。基因平衡器还将允许进行目前尚不具备的更复杂的基因实验 在 C. briggsae 中可行。最后，具有“安全港”着陆位点的菌株，用于将 DNA 引入指定的区域。 将产生并验证 C. briggsae 基因组中的位置。这些菌株将允许受控， 将单拷贝插入克隆可重复地引入 C. briggsae，并允许进行一系列实验 操作，包括两个物种之间的基因“节点交换”，以及为以下目的开发的试剂的测试 线虫直接存在于 C. briggsae 中。这些目标共同将产生消除重要障碍的关键工具 对该研究有机体进行遗传分析。