All higher eukaryotic genomes are composed to a large measure of transposable elements that continually attempt to expand their numbers even further. These elements can be thought of as intracellular parasites. While it is generally assumed that transposable elements insert more or less at random, a growing number of elements have been shown to minimize their effects on the host by evolving site-specificity. The model systems used in this research are the R1 and R2 non-LTR retrotransposable elements, which insert specifically into the 28S rRNA genes of many animals but have been studied most extensively in insects. The hundreds of tandemly arranged rRNA genes (the rDNA loci) of eukaryotes undergo dynamic processes of recombination to eliminate variation within the locus. Yet throughout their history, R1 and R2 have stably maintained their presence in the rRNA genes indicating they are well-adapted to exploit the recombinational and regulatory mechanisms devised by the cell to synthesize rRNA. The objectives of this research are to study the rDNA genes and their R1and R2 insertions in several Drosophila species at three levels. The first objective is to define the changes that have occurred in specific rDNA loci over defined periods of time. Large segments of the rDNA loci from two replicate lines of D. melanogaster that have been separated by over 400 generations will be recovered on a series of overlapping recombinant DNA clones assembled using the 5' marked R1 and R2 elements as reference points. Detailed comparisons of the extended regions will enable a first view of the specific patterns of recombination and of the distribution of the retrotransposition events that have given rise to the many changes known to have occurred between these lines. Second, natural populations of D. simulans will be screened to determine the frequency with which R2 elements are active as well as to characterize the size and structure of the rDNA loci. These studies will be conducted in D. simulans because this sister species of D. melanogaster has no rDNA units on the Y chromosome and populations with active R2 elements are readily obtained. Third, public data made available through whole genome shot-gun sequencing efforts of 12 Drosophila species as well as those of other insects will be used to score the nucleotide variation within the rDNA loci of various animals. The goal will be to establish the approaches that can be used to compare the mechanism and efficiency of concerted evolution of the rDNA loci. These studies will enable a greater understanding of the fluctuation in size, the regulation of expression, and the recombinational processes that give rise to both the sequence uniformity and the segmental changes that occur in the rDNA locus over time. They will also increase our understanding of the delicate balance that is reached between higher organisms and these intracellular parasites.
The genomes of all higher organisms are in a constant battle with internal parasites called mobile or transposable elements. Between 10% and 90% of total genomic DNA from different organisms is composed of these elements. This research focuses on a model system that has the advantage that the mobile elements specifically insert into one location of the genome: the tandemly repeated ribosomal RNA genes (rDNA locus). The model organisms are several fruit fly species (Drosophila). The studies include short term laboratory experiments, population experiments, and the utilization of genomic sequence data to follow the mobile elements being inserted into and deleted from the rDNA locus, as well as how the rDNA locus changes as a result of these insertions. This knowledge will help researchers both control and exploit these elements for the advantage of mankind. The project will also serve to further the education of high school science teachers, undergraduates, and graduate students.
