Novel approaches to map DNA replication traffic in a genome-wide scale

在全基因组范围内绘制 DNA 复制流量图的新方法

• 批准号: 9923689
• 负责人: Dieter Meinrad Egli
• 金额: $ 20.53万
• 依托单位: COLUMBIA UNIVERSITY HEALTH SCIENCES
• 依托单位国家: 美国
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-05-01 至 2022-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9923689
• 关键词: ATAC-seq; Address; Affect; Aging; Asians; Bioinformatics; Biological Phenomena; Biological Process; Bromodeoxyuridine; Cell Proliferation; Cells; Cellular biology; ChIP-seq; Communities; Computer software; Computing Methodologies; Cultured Cells; Custom; DNA; DNA Markers; DNA Modification Process; DNA Replication Timing; DNA Sequence; DNA analysis; DNA biosynthesis; DNA replication fork; DNA sequencing; DNA-Directed DNA Polymerase; Data; Detection; Development; Disease; Drops; Family; Genetic; Genome; Genomics; Goals; Human; Human Genome; Immunoprecipitation; Knowledge; Link; Location; Malignant Neoplasms; Maps; Measures; Methodology; Methods; Modeling; Modification; Names; Nucleotides; Optics; Pattern; Phase; Physiologic pulse; Positioning Attribute; Price; Protocols documentation; Publishing; Replication Initiation; Reproducibility; Resolution; Resources; Series; Signal Transduction; Technology; Testing; Time; Tissues; base; cell type; computational pipelines; cost effective; deep neural network; electrical property; epigenomics; experience; genome integrity; genome-wide; genome-wide analysis; insertion/deletion mutation; insight; nanopore; new technology; novel; novel strategies; nucleotide analog; sequencing platform; single molecule; stem cell differentiation; tumor progression

PROJECT SUMMARY The overarching goal of the project is to establish novel genomics and bioinformatics approaches to model patterns of DNA replication in cells. It is known that the patterns of DNA replication are intimately linked to the cell type. These differences between cell types are relevant to the integrity of the genome during cell type transitions. For example, we recently found that damage during DNA replication is increased during the induced transition from one cell type to another. However, there is a lack of methodology to observe replication patterns in human cells. DNA replication differs between different cell types in the location of initiation, the direction of fork progression, and the timing of initiation and completion. There is currently no method that can comprehensively map the progression of DNA replication to the genome. Because of the importance of DNA replication in cell proliferation, there is need for the development of such methods. To be able to examine the progression of DNA polymerases in human cells, we will develop a novel methodology to map DNA replication genome-wide, by incorporating nucleotide analogs during DNA replication, and sequencing the resulting DNA molecules by Nanopore sequencing and recording the electrical signals. In parallel, we will develop novel bioinformatics approaches to reliably examine the electrical signals and identify bases or regions of DNA replication, for comparison between different cell types, or between healthy and diseased tissues. Successful establishment of this technology will greatly increase our knowledge of replication, genetic stability and cell proliferation, and allow the community to characterize differences in the progression of DNA replication between cell types.

项目总结 该项目的总体目标是建立新的基因组学和生物信息学方法来模拟 细胞内DNA复制的模式。众所周知，DNA复制的模式与 单元类型。这些细胞类型之间的差异与细胞类型期间基因组的完整性有关 过渡。例如，我们最近发现，DNA复制过程中的损伤在诱导过程中增加 从一种细胞类型过渡到另一种细胞类型。然而，缺乏观察复制模式的方法 在人类细胞中。DNA复制在不同类型的细胞之间在起始位置、方向上有所不同 分叉进程，以及启动和完成的时间。目前还没有方法可以 全面地将DNA复制的进程映射到基因组。因为DNA的重要性 在细胞增殖复制方面，有必要发展这样的方法。为了能够检查 关于DNA聚合酶在人类细胞中的研究进展，我们将开发一种新的方法来绘制DNA复制图谱 在基因组范围内，通过在DNA复制过程中加入核苷酸类似物，并对产生的DNA进行测序 通过纳米孔对分子进行测序并记录电信号。同时，我们将开发新的 可靠地检查电信号和识别DNA碱基或区域的生物信息学方法 复制，用于不同细胞类型之间的比较，或健康组织和患病组织之间的比较。成功 这项技术的建立将极大地增加我们对复制、遗传稳定性和细胞的知识 增殖，并允许社区表征不同的DNA复制进程的差异 单元类型。