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.

项目概要/摘要 DNA 复制遵循确定的时空程序，其中基因组的不同部分在 S期的不同时间，DNA复制计时程序与基因组调控相互作用。 也影响基因组的稳定性和异常的复制时间。 尽管 DNA 复制调控对细胞和肿瘤发生很重要。 生物生物学，我们对 DNA 序列和分子机制的了解非常有限 同样，目前还不清楚真核DNA复制计时程序是如何进行的。 一般来说，控制与基因表达的调节和表观基因组相交叉。 继续开发新的实验和计算方法来测量全基因组 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。 揭示控制复制时间的序列元件并研究其作用机制 （Koren 等人，Cell 2014；Ding 等人，Nature Communications 2021；NIH 主任新创新者奖 DP2- GM123495）。在此 MIRA 应用程序中，我们将：1）生成人类复制时间的新数据集，即 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联系起来 以一种新颖而强大的方式进行调控 2）利用我们先前和并发的复制定时遗传。 映射以实验性地编辑控制复制时间的 DNA 序列。 一些表观基因组分析和基因实验将揭示其机制和后果 作为其中的一部分，我们还将开发一种新方法“perturb-RT”来调节复制时间。 3）继续我们最近的 通过联合测量复制时间和基因表达，成功分析单细胞复制时间 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。 我们的工作将对 DNA 复制计时和细胞分化领域做出重大贡献。 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，揭示复制时间的新见解 监管及其后果。