Abstract:
The ribosomal DNA genes (rDNA) form one of the genome's most conserved families of genes. They are organised in clusters of tandemly repeated units, and this repetitive nature and its high transcription rates makes the rDNA cluster a region of instability. In particular, the high transcription rate makes the cluster vulnerable to collisions between the transcription and replication machineries. The resulting instability is regulated by a mechanism that can increase recombination between rDNA units. However, recombination can occur between misaligned units, with this unequal recombination producing copy number variation. Such copy number variation has been reported across species, organisms, populations and even tissues. In this project, I wanted to evaluate how rDNA copy number distribution is influenced by the dynamics of selective pressure on copy number, the type of recombination event, and the length of misalignment produced during unequal recombination. I chose to evaluate this in haploid S. cerevisiae as rDNA dynamics are best characterized in this species. I developed a discrete-generation model with two steps to model these dynamics. The steps are selection and unequal non-reciprocal recombination. Probability distribution functions that describe misalignment probabilities for duplications and deletion events during non-reciprocal recombination were estimated using data from previous studies and then used in the model. Tests were made to ensure the model implementation works as expected. This model was supplemented by experimental determination of rDNA copy number distribution in a haploid S. cerevisiae population using ddPCR quantification. The measured distribution was then used to fit the model and compare different model versions. Overall, the assessed model had a reasonable fit to the experimental data, although improvements in the functions that describe selection and misalignment during deletion events may be able to provide a better fit. Surprisingly, under the evaluated conditions there were no improvements in models that allow recombination rate to change with different copy numbers even though this has been experimentally observed to occur. Further testing will be required to establish the cause of this result.