Interspersed repetitive elements, including Alu and LINE1 (LI) elements, make up 45% of the human genome, yet much remains unknown about their origins and dynamics. There is evidence that these elements affect the distribution of genetic diversity across the genome because of their influence on processes like recombination. The goals of this project are to build upon the knowledge gained from the previous funding period in order to pursue questions about the origins of Alu and LI elements and about their effects on patterns of genomic diversity. Using a series of PCR and sequencing experiments, we will evaluate the effects of gene conversion on Alu diversity. We will assess linkage disequilibrium patterns in 50 genomic regions to test the hypothesis that Alu elements mediate homologous recombination. We will undertake comparisons of human and chimpanzee genomes to test the hypothesis that Alu elements are important mediators of unequal crossover events, deleting and duplicating genes. We predict that LI elements, because of their observed distribution and their lower density in the genome, function less frequently as mediators of unequal crossover. We have designed a series of experiments to test the hypothesis that Alu elements insert into the genome in an endonuclease-independent fashion and may therefore participate in the repair of double-stranded DNA breaks. Finally, we will apply newly developed methods to determine whether natural selection has been operating on Alu and LI elements in the human genome. Factors like gene conversion and recombination exert important effects on patterns of genomic diversity, which in turn influence patterns of linkage disequilibrium in the genome. The proposed research, which will help to explore the influence of repetitive elements on genomic diversity, will thus have important implications for the use of linkage disequilibrium in localizing disease-causing genes. Our understanding of genetic disease will also be enhanced by a better understanding of the role of these elements in DNA repair and in gene duplication and deletion.
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