The Genetic Basis of Human DNA Replication Timing

项目摘要/摘要 DNA复制遵循定义的时空程序，在该程序中，基因组的不同部分以 S时期的不同时期。DNA复制计时程序与基因组调节接口，同时 也影响着基因组的稳定性和突变格局。关联了异常的复制时间 有遗传性疾病和肿瘤形成。尽管DNA复制调控对细胞和 生物生物学，我们对DNA序列和分子机制的了解非常有限 具体说明了真核DNA复制计时程序。同样，目前仍不清楚复制的时间安排如何 控制与基因表达的调节以及总体上与表观基因组相交。我的实验室有，而且 继续开发新的实验和计算方法来测量全基因组 复制计时。我们还开创了一种独特的方法，将复制时间与人类基因变异联系起来 为了揭示控制复制计时的序列元件并研究它们的作用机制 (Korn等人，Cell 2014；Ding等人，自然通信，2021；NIH主任的新创新者奖DP2- GM123495)。在这个Mira应用程序中，我们将：1)生成人类复制时间的新数据集 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学联系起来 以一种新颖而有力的方式进行监管。2)利用我们之前和当前的复制时间遗传 映射以便实验性地编辑控制复制计时的DNA序列。这之后将是 几种表观基因组分析和遗传实验将揭示 复制时间调节。作为这项工作的一部分，我们还将开发一种新的方法，“扰动RT”，以 系统地筛选控制复制计时的新序列元件。3)继续我们最近的 通过联合测量复制时序和基因表达来成功分析单细胞中的复制时序 在相同的单细胞中。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。我们的工作将极大地促进DNA复制计时和 此外，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， 破译人类复制计时的遗传基础，并揭示复制计时的新见解 监管及其后果。

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.