Mobile elements make up nearly half of the human genome. They are a significant cause of genetic disease as a result of both de novo insertion as well as mediation of nonhomologous recombination and deletion. We propose to build on our previous research to further understand the effects of mobile elements on the generation of genetic diversity in human and non-human primate genomes. We have developed a new technique, based on second-generation high-throughput sequencing, to simultaneously ascertain and genotype all members of mobile-element subfamilies in large samples of individuals. We will apply this technology to 42 large Utah pedigrees to directly estimate, for the first time, the rate of Alu retrotransposition in the human genome. We will also use these pedigrees to explore the relationship between mobile elements and the generation of de novo copy number variants. We will genotype thousands of Alu insertion polymorphisms in a diverse sample of 500 humans. Because our new technique identifies all members of each subfamily, rare insertions will be identified so that an unbiased frequency spectrum of insertion polymorphisms can be analyzed. These data will allow us to search for active Alu elements in the human genome, and they will allow us to test several key hypotheses about ancient human evolutionary history. We will take advantage of the availability of several non-human primate genome sequences to test the effects of mobile elements on insertions and deletions of genomic material during the evolution of these species. We will also examine the roles of mobile elements in mediating transduction events in humans and non-human primates, as this is an important source of new genetic material in genomes.

Public Health Relevance

Mobile elements account for about half of our genome, and they have been shown to cause human disease by disrupting or deleting genes. We will study a large number of mobile elements to understand how they influence other elements of the genome, and we will use mobile elements to test hypotheses about the history and evolution of human populations and non-human primate species.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
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Genetic Variation and Evolution Study Section (GVE)
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Eckstrand, Irene A
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University of Utah
Schools of Medicine
Salt Lake City
United States
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Jordan, Vallmer E; Walker, Jerilyn A; Beckstrom, Thomas O et al. (2018) A computational reconstruction of Papio phylogeny using Alu insertion polymorphisms. Mob DNA 9:13
Gilbert, Clément; Feschotte, Cédric (2018) Horizontal acquisition of transposable elements and viral sequences: patterns and consequences. Curr Opin Genet Dev 49:15-24
Baker, Jasmine N; Walker, Jerilyn A; Denham, Michael W et al. (2018) Recently integratedAluinsertions in the squirrel monkey (Saimiri) lineage and application for population analyses. Mob DNA 9:9
Al-Agha, Abdulmoein Eid; Ahmed, Ihab Abdulhamed; Nuebel, Esther et al. (2018) Primary Ovarian Insufficiency and Azoospermia in Carriers of a Homozygous PSMC3IP Stop Gain Mutation. J Clin Endocrinol Metab 103:555-563
Steely, Cody J; Baker, Jasmine N; Walker, Jerilyn A et al. (2018) Analysis of lineage-specificAlusubfamilies in the genome of the olive baboon,Papio anubis. Mob DNA 9:10
Gardner, Eugene J; Lam, Vincent K; Harris, Daniel N et al. (2017) The Mobile Element Locator Tool (MELT): population-scale mobile element discovery and biology. Genome Res 27:1916-1929
Walker, Jerilyn A; Jordan, Vallmer E; Steely, Cody J et al. (2017) Papio Baboon Species Indicative Alu Elements. Genome Biol Evol 9:1788-1796
Feusier, Julie; Witherspoon, David J; Scott Watkins, W et al. (2017) Discovery of rare, diagnostic AluYb8/9 elements in diverse human populations. Mob DNA 8:9
Steely, Cody J; Walker, Jerilyn A; Jordan, Vallmer E et al. (2017) Alu Insertion Polymorphisms as Evidence for Population Structure in Baboons. Genome Biol Evol 9:2418-2427
Baker, Jasmine N; Walker, Jerilyn A; Vanchiere, John A et al. (2017) Evolution of Alu Subfamily Structure in the Saimiri Lineage of New World Monkeys. Genome Biol Evol 9:2365-2376

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