Clark 9806655 Variation in the level of expression of a gene exists in populations in two different forms. Differences in the gene itself, including DNA sequences up- and downstream from the gene, play a role in determining the rate and stability of transcripts, so such variation can clearly have functional consequences. Gene expression is mediated by the assembly of transcription complexes, which involve numerous components which in turn are products of other genes. Variation in any of these genes, which may be remote from the primary target gene, can also have clear functional consequences. The dichotomy between variation that is in or near the gene (cis) vs. that which is remote from the gene (trans) is important on three levels. First, the remarkable sequence similarity of genes from such morphologically distinct species as humans and chimpanzee, suggest that regulatory changes are critical in determining the differences between species. Second, the issue of cis vs. trans is important from the perspective of theoretical population genetics, which says that clusters of very tightly linked genes will have different population dynamics from unlinked genetic differences. Third, we expect trans-regulatory variation to exhibit effects on many genes, and having such manifold or pleiotropic effects also impacts the tendency of a population to maintain variation in such genes. We propose four experiments to quantify and characterize the cis and trans differences among lines of fruit flies that account for variation in the expression of a series of metabolic enzymes. The first objective is to perform a mapping study of metabolic trait variation in D. melanogaster. These genetic maps will tell us the number of significant trans factors for each trait and the relative contributions of cis vs. trans effects to the variance in each trait. The second experiment is to quantify the magnitude of variation of metabolic traits among different environments. This experiment will reveal whether particular genomic segments (cis and trans) are responsible for differential response to environmental stresses for each metabolic phenotype. The third experiment will use hybrids between two different species of Drosophila to ask whether the divergence between species in gene expression is caused by cis elements or in trans-acting factors. This will be like the first mapping experiment, except that lines of flies having portions of their genomes from two different species will be used. Comparison of the regulatory variation within species to that between species will reveal many attributes of the ways differences in gene expression change between species. Finally, we will develop mathematical models of cis and trans regulatory variation to get a better understanding of the advantages and disadvantages of the two modes of regulation.
