Research

Transpoable elements (TEs) are mobile genetic sequences that populate and parasitize all genomes, both eukaryotic and prokaryotic. TEs impose a multifaceted mutational burden on their host through insertional inactivation of host genes, production of structural mutations by ectopic recombination, and the imposition of DNA damage. Our research focuses on how the host genome responds to these fitness consequences of TE activity. We use Drosophila melanogaster as a genetic model, and much of our research focuses on the recent invasion of P-elements into the D. melanogster genome. 

Host Tolerance and Resistance of P-elements 

The P-element invasion as a genetic model for the evolution of tolerance and resistance. P-elements are DNA transposons that invaded North American populations of D. melanogaster around 1950 and quickly colonized all D. melanogaster genomes worldwide. In response to this invasion, the D. melanogaster host quickly evolved to repress P-element activity by producing P-element derived piRNAs in the germline. piRNAs enact transcriptional and post-transcriptional silencing of target TEs. Because piRNAs are transmitted only through the female germline, crosses between naive females who lack P-elements and do not produce regulatory piRNAs and colonized males who carry P-elements allow for examination of host tolerance of P-element activity. By contrast in the reciprocal cross, piRNAs are transmitted by colonized females and reveal the evolved resistance of the host. We therefore take advantage of both colonized and naive genomes to study tolerance and resistance of P-element activity by the host.

Ancestral variation in host tolerance of TEs.  Little is known about host tolerance factors that may reduce the fitness costs of TEs without directly regulating their activity. Through genome-wide association (GWAS), we have uncovered multiple genomic regions that determine differences in host tolerance of P-element activity among the Drosophila Synthetic Population Resource, a panel of naive recombinant inbred lines (right). Causative alleles and variants that produce these QTL peaks (right) correspond to natural variants that may have conferred tolerance to D. melangoster after the P-element invaded. They also pave the way for examining whether host tolerance evolves after new TEs invade.

DNA damage response and host tolerance. One host factor that could determine host tolerance of TE activity is the sensitivity of host DNA damage response. Indeed, we have discovered that p53, a conserved eukaryotic protein involved in DNA damage response and induction of apoptosis, is induced in the presence of P-element activity (right, pink). We are interested in components of the DNA damage that influence that sensitivity of germline cells to P-element induced DNA damage,  as well as developmental regulators of oogenesis that may promote oocyte production despite the occurence of DNA damage.

piRNA mediated evolution of host-resistance. As we describe in our recent review, resistance of P-element activity in natural populations of D. melanogster likely evolved by the transposition of P-elements into piRNA producing sites known as piRNA clusters. Using forward simulations we have discovered that piRNA mediated silencing evolves rapidly in simulated populations, and that P-element insertions into piRNA clusters are beneficial mutations that increase in frequency by positive selection. In conjunction with our simulation models we are examining the presence and polymorphic frequency of P-element insertions in the Drosophila genetic reference panel, a group of colonized wild-derived inbred strains. 

Selection for Host Repression

In forward simulations higher fitness costs of hybrid dysgenesis (D) are associated with stronger selection for repression, as indicated by higher polymorphic frequencies of repressive alleles.

An important unanswered question in the evolution of host resistance is the degree to which different fitness effects of TEs, such as deleterious mutations, ectopic recombination and hybrid dysgenesis, select for repression in the host. Our forward simulations suggest that the sterility associated with hybrid dysgenesis is an important factor that enhances positive selection on TE insertions in piRNA producing sites (left). We are testing these prediction using experimentally evolved strains that differ in the fitness costs of P-element induced hybrid dysgensis.  

Functional analyses of adaptively-evolving piRNA effector proteins. In eukaryotes, host repression of TEs is thought to evolve through the acquisition of mutations that initiate or enhance the production of regulatory piRNAs. Although insertion of TEs into piRNA producing sites play a fundamental role in the acquisition of repression, piRNA effector proteins are also required for transcription and processing of piRNAs and the silencing of target TEs. In Drosophila, many piRNA effector proteins exhibit signatures of ongoing adaptive evolution, yet the target of selection, in terms a protein function that is selected to change, remains unknown. Using interspecific complementation together with functional genomics, we are examining functional divergence of adaptively evolving piRNA effector proteins between D. melanogaster and its sister species D. simulans.












© Erin Kelleher 2013