Mechanisms of Repetitive Element Mediated Genomic Rearrangements

重复元件介导的基因组重排的机制

• 批准号: 9162833
• 负责人: Christine R Beck
• 金额: $ 9万
• 依托单位: BAYLOR COLLEGE OF MEDICINE
• 依托单位国家: 美国
• 财政年份: 2016
• 资助国家: 美国
• 起止时间: 2016-09-01 至 2017-08-04
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9162833
• 关键词: 17p11.2; Affect; Alu Elements; Animal Model; Automobile Driving; Award; Basic Science; Bioinformatics; Biological Assay; Biology; Boxing; Cells; Clinical; Complex; Consensus Sequence; Constitutional; Copy Number Polymorphism; DNA Repair; DNA Repair Pathway; DNA Sequence Rearrangement; DNA replication fork; Data; Data Set; Development; Diagnostic; Disease; Doctor of Philosophy; Elements; Enzymes; Event; Faculty; Family member; Fanconi Anemia Complementation Group A Protein; Fostering; Foundations; Genes; Genetic Recombination; Genome; Genome Stability; Genomic Instability; Genomics; Goals; Guanine + Cytosine Composition; Human; Human Cell Line; Human Genetics; Human Genome; Insertional Mutagenesis; Investigation; Lead; Length; Location; Malignant Neoplasms; Mediating; Medicine; Mentors; Mentorship; Methodology; Methods; Michigan; Molecular Genetics; Nature; Nonhomologous DNA End Joining; Nucleotides; Participant; Pathway interactions; Patients; Phase; Play; Ploidies; Point Mutation; Population; Positioning Attribute; Prevalence; Process; Publishing; Recurrence; Repetitive Sequence; Reporter; Research; Research Personnel; Research Training; Retrotransposon; Role; Saccharomyces cerevisiae; Saccharomycetales; Sequence Homology; Smith Magenis syndrome; Study models; Syndrome; Techniques; Testing; Training; Training Programs; Universities; Variant; Work; Yeasts; abstracting; base; collaborative environment; college; design; homologous recombination; human genomics; improved; nuclease; proband; programs; repaired; skills; success; tissue culture; tool; tumor; yeast genetics

Project Summary/Abstract We have prepared a comprehensive training program that will transition a successful postdoctoral researcher to an independent faculty position focused on discerning the mechanisms underlying genomic rearrangements, specifically with relation to repetitive elements. The applicant has a PhD in Human Genetics focused on mobile element biology and variation from the University of Michigan, and in the last three and a half years has utilized molecular genetics and genomics to examine structural variation in personal human genomes, publishing 14 articles in human genetics and copy number variation from her postdoctoral work. Here, she will extend her extensive skill set to include genomic analysis and bioinformatics approaches to large data set manipulations as well as training in yeast genetics. These techniques will be developed and employed over a two-year program of mentored research and training followed by a three-year research program detailed in this proposal. The training program herein will utilize a trio of advisors to train the researcher in genomic analysis, bioinformatics, and yeast genetics to investigate the mechanisms underlying non-recurrent genomic rearrangements, specifically those mediated by Alu elements. Dr. James R. Lupski and Dr. Grzegorz Ira will provide mentorship for the award, and will train the researcher in human genetics and genomics and yeast manipulation, respectively. Dr. Lupski is internationally recognized for his work in copy number variation and mechanisms of genomic change as well as personal genomics. Dr. Ira is a leader in the field of recombination and is a talented and well-published researcher who specializes in DNA repair research utilizing Saccharomyces cerevisiae. The mentors will provide a supportive environment for the success of the candidate and her research plan, and will aid in her transition to independence. The Department of Molecular and Human Genetics at Baylor College of Medicine is an ideal location for this work, with diverse and varied expertise and a highly collaborative environment fostered by regular seminars ranging in focus from clinical to basic science research. Although much work has described the mechanism of non-allelic homologous recombination leading to structural variation of the human genome, a great deal remains unanswered regarding the mechanisms of non- recurrent rearrangements. Importantly, many non-recurrent structural variants have breakpoints that localize within Alu elements, and these sequences are enriched at the junctions of rearrangements. Therefore, we propose three aims to define the role of repetitive elements, specifically Alu sequences, in generating genomic rearrangements: (1) Determination of the repair pathways mediating non-recurrent rearrangements, specifically those where Alu elements play a role (2) Determine key parameters of Alu elements participating in rearrangements, to query these determinants in a budding yeast assay, and to distinguish regions of the human genome prone to such events (3) to identify the role enzymes regulating repetitive element template switches in yeast play in genomic stability of Alus in human cells. Many of the methodologies required for these analyses are not the candidate's current expertise. Therefore, the training in additional techniques is necessary for this research plan. This experimental methodology presented in this proposal can be utilized to determine how other structural features can predispose to genomic rearrangements, and thus will lay a foundation for future research plans.

项目概要/摘要 我们准备了一个全面的培训计划，将帮助一名成功的博士后过渡 独立教职研究员，专注于辨别基因组背后的机制 重新排列，特别是与重复元素相关的重新排列。申请人拥有人类遗传学博士学位 密歇根大学专注于移动元素生物学和变异，在过去的三年和一年中 半年来利用分子遗传学和基因组学来检查人类的结构变异 她在博士后工作中发表了 14 篇关于人类遗传学和拷贝数变异的文章。 在这里，她将扩展她广泛的技能，包括基因组分析和生物信息学方法 数据集操作以及酵母遗传学培训。这些技术将得到开发和应用 为期两年的指导性研究和培训计划，随后是一项详细的三年研究计划 在此提案中。 本文的培训计划将利用三名顾问来培训研究人员进行基因组分析， 生物信息学和酵母遗传学研究非复发基因组的机制 重排，特别是由 Alu 元素介导的重排。 James R. Lupski 博士和 Grzegorz Ira 博士将 为该奖项提供指导，并将对研究人员进行人类遗传学、基因组学和酵母方面的培训 分别操纵。 Lupski 博士因其在拷贝数变异方面的工作而获得国际认可 基因组变化的机制以及个人基因组学。 Ira博士是重组领域的领导者 是一位才华横溢且发表了大量论文的研究人员，专门从事利用 DNA 修复研究 酿酒酵母。导师将为项目的成功提供支持性环境 候选人和她的研究计划，并将帮助她过渡到独立。分子系 贝勒医学院的人类遗传学和人类遗传学是这项工作的理想地点，具有多种多样的 定期研讨会所营造的专业知识和高度协作的环境，重点关注从临床到 基础科学研究。 尽管许多工作已经描述了非等位基因同源重组的机制 尽管人类基因组的结构变异，但有关非变异机制的大量问题仍未得到解答。 经常性的重新排列。重要的是，许多非经常性的结构变体都有本地化的断点 Alu 元件内，这些序列在重排的连接处富集。因此，我们 提出三个目标来定义重复元素（特别是 Alu 序​​列）在生成中的作用 基因组重排：（1）介导非复发性修复途径的确定 重排，特别是 Alu 元素发挥作用的重排 (2) 确定 Alu 的关键参数 参与重排的元素，以在芽殖酵母测定中查询这些决定因素，以及 区分人类基因组中容易发生此类事件的区域 (3) 确定酶的作用 调节酵母中重复元件模板开关对人类 Alus 基因组稳定性的影响 细胞。这些分析所需的许多方法并不是候选人当前的专业知识。 因此，本研究计划需要额外技术的培训。这个实验 本提案中提出的方法可用于确定其他结构特征如何 易发生基因组重排，从而为未来的研究计划奠定基础。