Mechanisms of Repetitive Element Mediated Genomic Rearrangements

Beck, Christine

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.

Public Health Relevance

Genomic rearrangements are a common cause of variation in the population, and can lead to disease. The underlying mechanisms of these rearrangements are often poorly understood. Investigating how structural variation occurs can inform on mechanisms of cancer, will help facilitate development of improved diagnostic tools, and may find targets for potential therapies moving forward.