Chromatin-mediated mechanisms of genome integrity

染色质介导的基因组完整性机制

• 批准号: 10380859
• 负责人: David M MacAlpine
• 金额: $ 39.09万
• 依托单位: DUKE UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2018
• 资助国家: 美国
• 起止时间: 2018-04-01 至 2023-03-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10380859
• 关键词: Biochemical; Cell Cycle; Cell model; Chromatin; Chromatin Structure; Chromosomes; Collaborations; DNA; DNA Binding; DNA Repair; DNA biosynthesis; DNA replication fork; DNA replication origin; Data; Drosophila genus; Environment; Epigenetic Process; Event; Failure; Gene Expression; Genetic Transcription; Genome; Genomic Instability; Genomic approach; Genomics; In Vitro; Laboratories; Lead; Mediating; Nonhomologous DNA End Joining; Nucleosomes; Peptide Initiation Factors; Population; Positioning Attribute; Process; Replication Initiation; Replication Origin; Research; Saccharomyces cerevisiae; Site; Source; Structure; Yeasts; experimental study; genome integrity; genome-wide; helicase; homologous recombination; insight; novel strategies; preservation; programs; recombinational repair; reconstitution; repaired; transcription factor; tumorigenesis; yeast genome

Abstract Our research is focused on elucidating the mechanisms by which the local chromatin environment influences DNA- templated processes including DNA replication, transcription and DNA repair. While considerable progress has been made in our understanding of the mechanisms that direct DNA replication in vitro, we know very little about how start sites of DNA replication (origins) are selected and regulated in the context of the chromosome. The genomic approaches that my research group have pioneered have provided new insights into the mechanisms by which the local chromatin state and structure (nucleosome and transcription factor occupancy) influences key steps in regulating the DNA replication program in multiple species including S. cerevisiae and Drosophila. We have recently developed a novel approach to `footprint' a eukaryotic genome – simultaneously revealing genome- wide occupancy of DNA for both nucleosomes and smaller DNA binding factors (e.g. initiation and transcription factors). Unlike biochemical reconstitution experiments utilizing one or two defined DNA templates, we are able to comprehensively view the cell cycle regulated cascade of chromatin changes that occur surrounding each origin of replication in the yeast genome. Our future research will focus on identifying and characterizing the chromatin mediated events required for initiation of DNA replication following helicase loading. We will also investigate how chromatin structure is re-established throughout the genome to preserve epigenetic integrity following passage of the DNA replication fork. DNA replication is also a potent source of double-stranded breaks (DSB) which, if not repaired, may lead to genomic instability. We are uniquely positioned to identify and understand the dynamics of chromatin structure following the induction of site-specific DSBs and their subsequent repair by homologous recombination or non-homologous end joining. Finally, in collaboration with the Hartemink laboratory (Duke, CS) we are using synchronous populations of yeast proceeding through the cell cycle to develop robust statistical ap- proaches that will enable us to model cell cycle-dependent changes in gene expression from chromatin occupancy data.

抽象的 我们的研究重点是阐明局部染色质环境影响 DNA 的机制 包括DNA复制、转录和DNA修复在内的模板化过程已经取得了相当大的进展。 尽管我们对体外指导 DNA 复制的机制有了一定的了解，但我们对此知之甚少。 如何在染色体背景下选择和调节 DNA 复制的起始位点（起点）。 我的研究小组开创的基因组方法为该机制提供了新的见解 局部染色质状态和结构（核小体和转录因子占用）影响关键 调节包括酿酒酵母和果蝇在内的多个物种的 DNA 复制程序的步骤。 最近开发了一种新方法来“足迹”真核基因组——同时揭示基因组—— 核小体和较小的 DNA 结合因子（例如起始和转录）广泛占据 DNA 与使用一两个确定的 DNA 模板的生化重建实验不同，我们能够 全面观察每个起源周围发生的细胞周期调节的染色质变化级联 我们未来的研究将集中于染色质的识别和表征。 我们还将研究解旋酶加载后启动 DNA 复制所需的介导事件。 染色质结构在整个基因组中重建，以在传代后保持表观遗传完整性 DNA 复制叉也是双链断裂 (DSB) 的一个重要来源。 修复，可能会导致基因组不稳定，我们具有独特的优势来识别和理解动态。 诱导位点特异性 DSB 及其随后通过同源修复后的染色质结构 最后，与 Hartemink 实验室（杜克大学，CS）合作。 我们正在使用同步进行细胞周期的酵母群体来开发强大的统计应用程序 这些方法将使我们能够模拟染色质占据导致的基因表达的细胞周期依赖性变化 数据。