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: 9620141
• 负责人: Christine R Beck
• 金额: $ 24.9万
• 依托单位: UNIVERSITY OF CONNECTICUT SCH OF MED/DNT
• 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 2020-12-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9620141
• 关键词: 17p11.2; Affect; Alu Elements; Animal Model; Automobile Driving; Award; Basic Science; Bioinformatics; Biological Assay; Biology; 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; International; 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; Repetitive Sequence; Reporter; Research; Research Personnel; Research Training; Retrotransposon; Role; Saccharomyces cerevisiae; Saccharomycetales; Sequence Homology; Smith Magenis syndrome; Study models; Syndrome; Talents; Techniques; Testing; Training; Training Programs; Universities; Variant; Work; Yeasts; 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.

项目总结/摘要 我们已经准备了一个全面的培训计划，将过渡到一个成功的博士后 研究员到一个独立的教师职位，专注于辨别基因组的机制 重组，特别是与重复的元素。申请人拥有人类遗传学博士学位 专注于移动的元素生物学和密歇根大学的变化，在过去的三年和一年中， 半年来，他利用分子遗传学和基因组学来研究个人人类的结构变异， 基因组，发表了14篇文章，人类遗传学和拷贝数变异从她的博士后工作。 在这里，她将扩展她的广泛的技能，包括基因组分析和生物信息学方法，以大 数据集操作以及酵母遗传学培训。这些技术将得到发展和应用 一个为期两年的指导研究和培训计划，然后是一个为期三年的研究计划详细 在这个提议中。 这里的培训计划将利用三位顾问来培训基因组分析方面的研究人员， 生物信息学和酵母遗传学来研究非复发性基因组的机制， 重组，特别是那些由Alu元素介导的。James R.卢普斯基和格热戈兹伊拉博士 为该奖项提供指导，并将在人类遗传学和基因组学以及酵母方面培训研究人员 操纵，分别。Lupski博士因其在拷贝数变异方面的工作而受到国际认可， 基因组变化的机制以及个人基因组学。伊拉博士是重组领域的领导者 他是一位才华横溢、发表过大量论文的研究人员，专门从事DNA修复研究， 酿酒酵母导师们将为项目的成功提供一个支持性的环境， 候选人和她的研究计划，并将帮助她过渡到独立。分子学系 贝勒医学院的人类遗传学是这项工作的理想地点， 专业知识和高度协作的环境，定期举办研讨会，重点从临床到 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导致基因突变的机制， 人类基因组的结构变异，大量的关于非- 经常性重排。重要的是，许多非复发性结构变异具有定位于 在Alu元件内，并且这些序列在重排的连接处富集。所以我们 我提出了三个目标来定义重复元件的作用，特别是Alu序列，在生成 基因组重排：（1）确定介导非复发性 重排，特别是那些Alu元素发挥作用的重排（2）确定Alu的关键参数 参与重排的元件，以在芽殖酵母测定中查询这些决定簇，以及 以区分人类基因组中易于发生此类事件的区域（3）以确定酶的作用 调控酵母中的重复元件模板开关在人类Alus基因组稳定性中的作用 细胞这些分析所需的许多方法不是候选人目前的专业知识。 因此，额外技术的培训对于本研究计划是必要的。该实验 本提案中提出的方法可用于确定其他结构特征如何能够 这将为未来的研究计划奠定基础。