RUI: Origins of Intron-Exon Structures

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The research project studies differences in the molecular structures of genes and genomes across a wide swath of organisms ranging from humans to parasites. In particular, the project seeks to answer the mystery of the origins of introns, intervening stretches of DNA that interrupt the genes of all eukaryotes, i.e., the organisms that have nucleated cells. By conducting the work at San Francisco State University, one of the most diverse comprehensive universities in the country, this work will support training in biological and computational sciences of individuals from underrepresented minority groups at early stages in their careers (undergraduate and masters students). The project seeks to answer the mystery of the origins of spliceosomal introns in eukaryotes. The vast majority of introns are DNA fragments inserted within protein-coding genes without a known function and with a quasi-random DNA sequence, raising the twin questions of (i) why are there introns; and (ii) how are introns created in evolution? To answer these questions, the project uses the strategy of identifying and studying recent cases of intron gain (creation of an intron) and loss (deletion of an intron from the genome). Recent gains and losses will be identified by direct genome-wide comparison between 50 groups of closely related organisms, as well as by comparison of individual intron sequences within the genomes of a larger set of 1000 organisms. These identified changes will be scrutinized to determine the molecular mechanisms that gave rise to these changes, the impact of these changes on production of gene products, and the overall impact of these changes on organismal fitness.