The Genetic Basis of Human DNA Replication Timing

人类 DNA 复制时间的遗传基础

• 批准号: 10543681
• 负责人: Amnon Koren
• 金额: $ 7.63万
• 依托单位: CORNELL UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-05-01 至 2024-01-01
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10543681
• 关键词: Award; Biological Assay; Biology; Cells; Chromosome Mapping; Communication; DNA Replication Timing; DNA Sequence; DNA biosynthesis; Data Set; Development; Elements; Experimental Genetics; Gene Expression; Gene Expression Regulation; Genes; Genetic; Genetic Diseases; Genetic Variation; Genome; Genome Stability; Genomic approach; Human; Human Genetics; Link; Measures; Molecular; Mutation; Nature; Other Genetics; Regulation; S phase; Specific qualifier value; United States National Institutes of Health; Work; cancer genetics; epigenome; epigenomics; genetic approach; genome resource; genome-wide; human DNA; insight; novel; novel strategies; programs; spatiotemporal; success; tumorigenesis

PROJECT SUMMARY / ABSTRACT DNA replication follows a defined spatiotemporal program in which different parts of the genome replicate at different times during S phase. The DNA replication timing program interfaces with genome regulation while also influencing the genome’s stability and mutational landscape. Abnormal replication timing is associated with genetic diseases and oncogenesis. Despite the importance of DNA replication regulation to cell and organismal biology, we have very limited understanding of the DNA sequences and molecular mechanisms that specify the eukaryotic DNA replication timing program. Similarly, it remains unclear how replication timing control intersects with the regulation of gene expression and with the epigenome in general. My lab has, and continues to, develop novel experimental and computational approaches for measuring genome-wide replication timing. We also pioneered a unique approach of linking replication timing to human genetic variation in order to reveal the sequence elements that control replication timing and study their mechanisms of action (Koren et al., Cell 2014; Ding et al., Nature Communications 2021; NIH Director’s New Innovator Award DP2- GM123495). In this MIRA application, we will: 1) generate a new dataset of human replication timing, the largest so far, and use a computational approach to link replication timing to gene expression and epigenomic regulation in a novel and powerful way. 2) Utilize our previous and concurrent replication timing genetic mapping in order to experimentally edit DNA sequences controlling replication timing. This will be followed by several epigenomic assays and genetic experiments that will reveal the mechanisms and consequences of replication timing regulation. As part of this, we will also develop a new approach, “perturb-RT”, to systematically screen for novel sequence elements controlling replication timing. 3) Continue our recent success of profiling replication timing in single cells by jointly measuring replication timing and gene expression in the same single cells. We will use this approach to study how replication timing and gene expression co-vary during cellular differentiation. Our work will substantially contribute to the field of DNA replication timing and beyond, by providing unprecedented genomic resources, introducing novel genetic and genomic approaches, deciphering the genetic basis of human replication timing, and revealing new insights into replication timing regulation and its consequences.

项目摘要 /摘要 DNA复制遵循定义的时空程序，其中基因组的不同部分在 在s阶段的不同时间。 DNA复制时间与基因组调节的接口，而 还影响基因组的稳定性和突变景观。异常复制时机是相关的 遗传疾病和肿瘤发生。尽管DNA复制对细胞的重要性很重要，并且 生物学，我们对DNA序列和分子机制的理解非常有限 指定了真核DNA复制时间计划。同样，还不清楚复制时间如何 对照与基因表达的调节和表观基因组的调节相交。我的实验室有， 继续，开发用于测量全基因组的新型实验和计算方法 复制时机。我们还开创了将复制时间与人遗传变异联系起来的独特方法 为了揭示控制复制时间和研究其作用机理的序列元素 （Koren等人，Cell 2014； Ding等人，自然通讯2021； NIH董事的新创新者奖DP2- GM123495）。在此MIRA应用程序中，我们将：1）生成人类复制时机的新数据集， 迄今为止最大的，并使用一种计算方法将复制时间与基因表达和表观基因组联系起来 以一种新颖而有力的方式进行调节。 2）利用我们以前的和并发的复制正时通用 映射以实验编辑控制复制时间的DNA序列。接下来是 几种表观基因组学测定和基因实验将揭示机制和后果 复制正时调节。作为此的一部分，我们还将开发一种新方法“ witturb-rt”，以 系统地筛选了控制复制时间的新型序列元素。 3）继续我们的最新 通过共同测量复制时间和基因表达，单个细胞中分析复制时间的成功 在同一单元中。我们将使用这种方法来研究复制时机和基因表达共同变化 在细胞分化过程中。我们的工作将大大促进DNA复制时机的领域和 除了提供前所未有的基因组资源，引入了新的遗传和基因组方法， 解释人类复制时间的遗传基础，并揭示对复制时间的新见解 监管及其后果。