Beyond ERCs: exploring catastrophic forms of rDNA instability in aging yeast

Abstract

Single-celled organisms grown in identical conditions have variable life spans. Identifying the factors that drive the inherent variability in life span is crucial for our understanding of aging at a fundamental level. Here, we revisit the role of chromosome XII instability as a source of life span variability in aging populations of the budding yeast, Saccharomyces cerevisiae. We followed populations of mother cells as they aged and quantified changes in karyotype, DNA content, and aberrant structures within the rDNA. We quantified the kinetics of rDNA amplification both as extrachromosomal rDNA circles (ERCs) and as structural forms that are not resolved on CHEF gels. We propose mechanistic models of rDNA instability that describe how both ERCS and other aberrant structures are generated and the unique affects they have on life span. One of the models, which we call Catastrophic IntraChromosomal Repair (CICR), follows the fate of a broken replication fork in the rDNA locus when the template used for repair has already been replicated. At the completion of replication, when all other replication forks have successfully terminated, single, unopposed replication forks remain in the rDNA generating branched DNA molecules that have profound consequences during mitosis and/or subsequent cycles. In addition to ERCs, CICR and related events are additional forms of rDNA instability that contribute to the life span variability in isogenic populations of aging yeast.