The activity of genes (gene expression) is precisely regulated in all living organisms, with genes varying in the timing, spatial distribution, and extent of activity. This research aims to investigate evolutionary divergence in gene expression between species. This will be accomplished using strains of the fruit fly, Drosophila, that are hybrids between two closely related species. These strains have been tested to identify genes with expression patterns that result from interactions between the portions of their genomes that come from the two parent species. This project will locate the precise genetic differences between these species that are involved in these interactions.
Gene expression results from complex interactions between genes, and between genes and environmental influences. Understanding how interactions within genomes contribute to physical characteristics of organisms, and how they change through evolution, is a critical step towards elucidating how biological systems are constructed and how they function. This research will generate opportunities for college students to experience and participate in original scientific research that lies at the interface of computational biology and genomics.
This project’s intellectual merit lies in the novel discoveries of how gene expression evolves between closely related species, and the regulation of gene expression in the cells in the testes that develop into sperm. Genes influence characteristics of organisms through the sequences of the RNAs and proteins that they encode, and through the timing and levels at which these molecules are produced, known as gene expression. Understanding the way that gene expression contributes to the morphological, physiological, and behavioral characteristics of organisms and the ways in which it can lead to new species is therefore central to our understanding of biology. The formation of new species is frequently driven by the accumulation of mutations that have beneficial effects within a population, but cause sterility or death when combined with genes from a different population; such mutations are called incompatibilities. In many animals, incompatibilities are frequently located on the X chromosome and cause sterility of male hybrids, while leaving female hybrids fertile and hybrids of both sexes otherwise viable. A general understanding of the formation of new species in animals therefore requires understanding the evolution of X-linked genes that function during spermatogenesis and render hybrid males sterile. Analysis of gene expression divergence between the fruit fly species D. simulans and D. mauritiana, revealed more extensive divergence in gene expression than previously appreciated for such closely related species, and showed that gene expression evolves more rapidly in males than in females. Furthermore, many differences between the sexes in gene expression are consistent with a model of sexual antagonism, where mutations have different fitness effects (such as beneficial vs. deleterious) in males and females, suggesting such antagonism may be common. These analyses showed that only 20% of evolutionary divergence in gene expression between these species results from mutations in DNA sequences near to the expressed gene (called cis-regulatory sequences), while 80% can be attributed to mutations in proteins encoded by other genes that modulate the effects of cis-regulatory sequences (called trans-regulatory factors). This project also discovered that these two components of gene expression (cis- and trans) evolve in different ways. This project discovered novel features of gene expression in D. melanogaster that are specific to the X chromosome and the cells of the testes that produce sperm. In the majority of cells in D. melanogaster males, gene expression along the entire X chromosome is increased to compensate for the difference in X chromosome copy-number between the sexes (one X in males, two in females). However, this project discovered that in the testes this X chromosome dosage compensation is absent. This indicates that spermatogenesis differs from other developmental processes in Drosophila such as larval growth. Second, in many species, in the testes the X chromosome is inactivated and gene expression from this chromosome is shut off. This project found that, contrary to the conclusions of previous research, during Drosophila spermatogenesis there is no such inactivation of the X chromosome. Because sex is determined in Drosophila by the X and Y chromosomes, males inherit an X chromosome from their mother and a Y chromosome from their father (as is the case in humans). This project discovered that under circumstances when male Drosophila inherit an X chromosome from their father and a Y chromosome from their mother, this affects the expression of hundreds of genes located on all chromosomes. The genes that changed expression mostly function only in the testes, indicating that gene regulation in the male germline is sensitive to the some aspect of chromosome conformation that results from inheritance via a male or a female. These results have broad impacts for our understanding of gene regulation and species formation. Perturbations in chromosome copy-number and the attendant effects on gene expression impact human health through both inherited conditions (such as Down’s Syndrome) and the changes in genome structure that accompany cancer cell progression. The discovery that the X chromosome is not compensated in the D. melanogaster testes impacts our understanding of the role of gene dosage in cellular and developmental processes and suggests that these cells may provide a model for how cells compensate for differences in gene dosage. In species with XY sex chromosomes, such as Drosophila and mammals, understanding spermatogenesis, how it evolves between species, and what drives the evolution of male-sterile incompatibilities is central to our understanding of species formation and biodiversity. Many of the patterns associated with the evolution of genes expressed in the Drosophila testes are also observed among testis-specific genes in mammals, including humans. A better understanding of spermatogenesis in Drosophila may therefore teach us about this process in humans, which may lead to improved understanding of male fertility and treatments for reduced fertility and sterility.
