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

项目总结/摘要 相同的基因组序列如何在发育过程中产生不同的细胞类型仍然是一个基本问题。 生物学中的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发育和疾病期间的分子概况。然而，在这方面， 一次从单个细胞监测各个模态冒着仅从单个细胞获得部分图片的风险。 复杂的监管网络。希望多模式单细胞基因组学工具来克服这种限制。 我最近发明了一种超高通量联合分析开放染色质和转录组的方法， 相同的单细胞（Paired-seq），并证明了其全面研究细胞的潜力， 来自异种脑组织的类型特异性调节程序。在K99/R 00申请中，我建议 进一步开发一套新的单细胞多组学工具来研究动态和细胞类型特异性的调控 哺乳动物发育期间的电路。我将提高配对测序的灵敏度和覆盖率， 从表型水平进行单细胞多组学分析的计算方法（Aim 1）。后来我 将进一步开发高通量单细胞联合分析组蛋白修饰/转录的方法， 与基因表达结合的因子（配对标签），用于从机制水平分析分子程序 （目标2）。最后，我将应用这些技术来研究动态和细胞类型特异性的分子程序， 哺乳动物发育中的生殖细胞，并在此过程中鉴定和验证新的调节剂（Aim 3）。 总的来说，这项建议的结果将为研究表观遗传程序提供新的技术， 复杂的组织，并在单细胞分辨率的发展过程中，并提供更完整的意见， 哺乳动物生殖细胞发育过程中的基因调控回路。我的职业目标是领导一个独立的 研究小组专注于整合新的实验和计算技术，以了解 控制哺乳动物发育的基本原则。在K99阶段，我将继续收到 实验和计算培训从我的博士后导师任博士和合作者/顾问 加州大学圣地亚哥分校和索尔克研究所的委员会。严格的指导支持和在 K99阶段将有助于我在R 00阶段过渡到独立调查员，并为 我未来的职业

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.