Chromatin-mediated mechanisms of genome integrity

染色质介导的基因组完整性机制

• 批准号: 9895833
• 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/9895833
• 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 模板的过程，包括DNA复制，转录和DNA修复。虽然取得了很大的进步 我们是为了理解在体外直接DNA复制的机制时，我们对此一无所知 在染色体的背景下，如何选择和调节DNA复制（起源）的开始位点。这 我的研究小组开创性的基因组方法为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）的影响键 在包括酿酒酵母和果蝇在内的多种物种中调节DNA复制程序的步骤。我们 最近已经开发了一种新型的方法来“足迹”真核基因组 - 很揭示了基因组 - DNA的广泛占核小体和较小的DNA结合因子的占用率（例如起始和转录 因解者）。与使用一个或两个定义的DNA模板的生化重构实验不同，我们能够 全面查看细胞周期调节的染色质变化的级联 在酵母基因组中复制。我们未来的研究将着重于识别和表征染色质 在解旋酶载荷后启动DNA复制所需的介导事件。我们还将调查如何 在整个基因组中重新建立了染色质结构，以保留经过的表观遗传完整性。 DNA复制叉。 DNA复制也是双链断裂（DSB）的潜在来源，如果不是 修复，可能导致基因组不稳定性。我们有独特的位置来识别和理解动态 诱导位点特异性DSB及其随后通过同源的修复后的染色质结构 重组或非理论结束。最后，与Hartemink实验室（Duke，CS）合作 我们正在使用整个细胞周期进行酵母菌的同步种群，以发展强大的统计AP- 可以使我们能够模拟来自染色质占用的基因表达的细胞周期依赖性变化 数据。