Ribosomal RNAs (rRNAs) in budding yeast are encoded by ~100-200 repeats of a 9.1kb sequence arranged in tandem on the long arm of chromosome XII, the ribosomal DNA (rDNA) locus. Two major features of the rDNA locus give it the unique potential to sense the environment and tune cellular response – high instability, and the wide range of copy number variation it can accommodate.
Because of the tandem nature of the repeats in the rDNA array, the high rates of transcription it needs to accommodate, and the difficulty of replicating repetitive sequences, the rDNA array is highly prone to double stranded breaks (DSBs) and homologous recombination, which leads to loss of repeats at a rate as high as 1 copy per cell division, making it one of the most unstable and fragile loci in the genome. Additionally, because the rDNA locus makes up ~60% of Chr XII, and ~10% of the genome, its dynamics can potentially regulate genome function. However, the mechanisms of regulation of instability and its consequences on cell physiology remain poorly understood.
Copy number (CN) of rDNA repeat units in eukaryotic cells is maintained far in excess of the requirement for ribosome biogenesis. In yeast, only about 50% of the ~150 rDNA repeats are actively transcribed to meet the translational needs of the cell. The extra, untranscribed copies are thought to contribute to stability and integrity of the locus by acting as a ‘foothold’ for repair enzymes and for contacts with other regions of the genome. These could involve, for example, differential recruitment of chromatin-modifying proteins to rDNA arrays with variable CN. This supports the idea that the effects of CN go well beyond rRNA production for ribosome biogenesis.
Thus, the hypervariablity of the locus combined with its ability to titrate various factors gives it the potential to act as a sensor of various conditions/stresses and in response, be a rapid and reversible source of variation for adaptation at the cellular and organismal levels. Despite its potential to affect cellular homeostasis, there are large gaps in our understanding of the regulation of this locus. What factors affect instability of the rDNA array? How is CN determined and maintained? What is the correlation between instability and CN? What are the consequences of having an abnormally expanded rDNA array? My goal is to develop and implement assays to gain insight into these important questions.