The Evolution of Gene Regulation in Drosophila.

Abstract

Differences in gene expression drive phenotypic diversity. At the level of transcription, these differences are largely controlled by the complex interplay between trans-acting factors and the cis-regulatory sequences to which they bind. In this dissertation, I characterized how the regulation of gene expression has evolved both within and between several species of the Drosophila lineage. I began by describing current methodology to accurately quantify allele-specific expression (ASE) from RNA-seq data, comparing two different methods and highlighting sources of bias. Using this methodology, I measured allele-specific differences in F1 hybrids made by reciprocally crossing two strains of D. melanogaster. These two sets of genetically-identical hybrids differed only by which strain contributed the maternal or paternal allele, allowing me to test the hypothesis that D. melanogaster do not imprint their genome. Next, for that same intraspecific comparison as well as two interspecific comparisons, I measured total and allele-specific gene expression to categorize regulatory differences across divergence times ranging from 0.01-2.5 million years ago. This allowed me to test the hypothesis that cis-regulatory differences account for a higher proportion of the total regulatory differences between species, as well as to determine how patterns for inheritance of gene expression differ across an evolutionary timescale. Because all of these comparisons were made using female whole flies, I tested the prevalence of sex- and tissue-specific differences using gene expression data from female and male carcass and gonad tissues between D. pseudoobscura and its closely-related subspecies D. p. bogotana and their F1 hybrids. I determined that one must use caution when inferring patterns of regulatory divergence in whole flies, as the integration over all different tissue types can mask the complexity of gene regulation in individual tissues. The work in this dissertation expands our knowledge of how the regulation of gene expression differs across a well-characterized lineage and will continue to drive further studies of these phenomena in even more distantly-related species.