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.

项目总结/摘要 DNA复制遵循一个确定的时空程序，其中基因组的不同部分以不同的速度复制。 在S期的不同时间。DNA复制定时程序与基因组调控相互作用， 也影响了基因组的稳定性和突变景观。异常复制计时与 遗传疾病和肿瘤发生。尽管DNA复制调控对细胞和 生物学，我们对DNA序列和分子机制的理解非常有限 指定真核生物DNA复制时间程序。同样，目前还不清楚复制时间 控制与基因表达的调节和一般的表观基因组相交。我的实验室有， 继续开发新的实验和计算方法来测量全基因组 复制定时。我们还开创了一种将复制时间与人类遗传变异联系起来的独特方法 为了揭示控制复制时间的序列元件并研究它们的作用机制， （Koren等人，Cell 2014; Ding等人，Nature Communications 2021; NIH主任新创新者奖DP 2- GM 123495）。在这个MIRA应用程序中，我们将：1）生成一个新的人类复制时间数据集， 迄今为止最大的，并使用计算方法将复制时间与基因表达和表观基因组 以一种新颖而有力的方式进行监管。2)利用我们以前和同时复制的时间遗传 映射，以便实验性地编辑控制复制定时的DNA序列。随后将 几个表观基因组测定和遗传实验，将揭示机制和后果， 复制时间调节作为其中的一部分，我们还将开发一种新的方法，“扰动RT”， 系统地筛选控制复制定时的新序列元件。3)继续我们最近的 通过联合测量复制时间和基因表达成功分析单细胞中的复制时间 在同一个细胞中。我们将使用这种方法来研究复制时间和基因表达如何共同变化 在细胞分化过程中。我们的工作将大大有助于DNA复制的时间， 除此之外，通过提供前所未有的基因组资源，引入新的遗传和基因组方法， 破译人类复制时间的遗传基础，并揭示对复制时间的新见解 规则及其后果。