Studying the Mammalian Regulatory Circuits by Developing Single-cell Multi-omics Technologies

通过开发单细胞多组学技术研究哺乳动物的调节回路

• 批准号: 10606883
• 负责人: Chenxu Zhu
• 金额: $ 24.9万
• 依托单位: NEW YORK GENOME CENTER
• 依托单位国家: 美国
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-07-01 至 2025-04-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10606883
• 关键词: Advisory Committees; Automobile Driving; Award; Binding; Biology; Brain; Cells; Chimeric Proteins; Chromatin; Clustered Regularly Interspaced Short Palindromic Repeats; Complex; Computational Biology; Computing Methodologies; Coupling; DNA Sequence; Data; Data Set; Detection; Development; Disease; Epigenetic Process; Focus Groups; Foundations; Funding; Future; Gene Expression; Gene Expression Regulation; Genetic; Genetic Transcription; Genome; Genomics; Germ Cells; Goals; Individual; Institutes; Investigation; Joints; Lead; Mentors; Methods; Modality; Molecular; Molecular Analysis; Molecular Profiling; Monitor; Mus; Organism; Outcome; Performance; Phase; Phenotype; Population; Positioning Attribute; Procedures; Process; Regulator Genes; Regulatory Element; Research; Research Personnel; Resolution; Risk; Running; Surveys; Technology; Time; Tissues; Training; brain tissue; career; cell type; comparative; epigenome; gene regulatory network; genomic tools; histone modification; improved; interdisciplinary approach; multimodality; multiple omics; new technology; novel; programs; single cell analysis; tool; transcription factor; transcriptome; virtual

Project Summary/Abstract How the identical genome sequence produces diverse cell types during development remains a fundamental question in biology. Recent technology advancements in single-cell genomics provided excellent opportunities to study the molecular profiles during development and in disease at unprecedented resolution. However, monitoring individual modalities from single cells at a time runs the risk of obtaining only partial pictures from the complex regulatory network. Multi-modal single-cell genomics tools would be desired to overcome this limitation. I recently invented a method for ultra-high-throughput joint analysis of open chromatin and transcriptome from the same single cells (Paired-seq) and demonstrated its potential for comprehensive investigations of the cell- type-specific regulatory programs from heterogenous brain tissues. In this K99/R00 application, I propose to further develop a set of new single-cell multi-omics tools to study the dynamic and cell-type-specific regulatory circuits during mammalian development. I will improve the sensitivities and coverages of Paired-seq and develop a computational method for single-cell multi-omics analysis from the phenotypic level (Aim1). Subsequently, I will further develop a method for high-throughput single-cell joint analysis of histone modifications/transcription factors binding with gene expression (Paired-tag) for analysis of molecular programs from the mechanistic level (Aim2). Finally, I will apply these technologies to study the dynamic and cell-type-specific molecular programs in mammalian developing germ cells, and to identify and validate novel regulators during this process (Aim3). Overall, the results from this proposal will provide new technologies for the study of epigenetic programs in complex tissues and during development at single-cell resolution, and providing more complete views of the gene regulatory circuits during mammalian germ cell development. My career goal is to lead an independent research group focusing on integrating novel experimental and computational technologies to understand the underlying principles controlling mammalian development. During the K99 phase, I will continue to receive experimental and computational training from my postdoctoral mentor Dr. Ren and collaborators/advisory committee at UC San Diego and the Salk Institute. The rigorous mentored support and results obtained in the K99 phase will facilitate my transition to an independent investigator in the R00 phase and lay the foundation for my future career.

项目摘要/摘要 相同的基因组序列在开发过程中如何产生各种细胞类型仍然是基本的 生物学问题。单细胞基因组学的最新技术进步提供了极好的机会 以前所未有的分辨率研究开发和疾病期间的分子谱。然而， 一次监视单个单元的单个模式 复杂的监管网络。需要多模式的单细胞基因组学工具来克服这一限制。 我最近发明了一种对开放染色质和转录组的超高通量关节分析的方法 相同的单细胞（配对seq），并证明了其对细胞的全面研究的潜力 来自异源脑组织的类型特异性调节程序。在此K99/R00应用程序中，我建议 进一步开发了一组新的单细胞多摩斯工具来研究动态和细胞类型的调节 哺乳动物发育过程中的电路。我将提高配对式的敏感性和覆盖范围，并发展 一种用于表型水平的单细胞多矩分析的计算方法（AIM1）。随后，我 将进一步开发一种用于组蛋白修饰/转录的高通量单细胞关节分析的方法 与基因表达（配对标签）结合的因素，用于分析机械水平的分子程序 （AIM2）。最后，我将应用这些技术来研究动态和细胞类型的分子程序 哺乳动物发育的生殖细胞，并在此过程中识别和验证新型调节剂（AIM3）。 总体而言，该提案的结果将为研究表观遗传计划的新技术提供 复杂的组织和在单细胞分辨率下的开发过程中，并提供了更完整的视图 哺乳动物生殖细胞发育过程中的基因调节回路。我的职业目标是领导独立 研究小组致力于整合新颖的实验和计算技术以了解 控制哺乳动物发展的基本原则。在K99阶段，我将继续收到 我的博士后导师Ren博士和合作者/咨询公司的实验和计算培训 加州大学圣地亚哥分校和萨尔克学院的委员会。严格的指导支持和在 K99阶段将促进我在R00阶段过渡到独立调查员，并为 我的未来职业。