Visualize and quantify rDNA instabilities in mammalian cells and mouse models
Ribosomal DNA (rDNA) encodes the 18S, 5.8S, and 28S RNA components of ribosomes, accounting for up to 70% of cellular transcription. Despite its central role in cellular function and known association with cancer and aging, quantifying rDNA instability in mammals remains challenging due to its repetitive organization and inherent heterogeneity. In this study, we developed murine rDNA FISH probes and genomic tools tailored for laboratory strains. The results confirmed the locations of rDNA clusters, uncovered marked inter-/intra-strain and inter-cell heterogeneity at rDNA loci in inbred mice and unstressed cells, and identified sources of spontaneous, replication-associated DNA double-strand breaks within rDNA. Focused mini-screens using DNA repair-deficient cells uncovered distinct contributions of homologous recombination, non-homologous end-joining, and the ATM-mediated DNA damage response in safeguarding rDNA stability. Together, these findings and tools provide a robust framework for assessing rDNA instability in mammalian cells and animal models with applications in aging and cancer research. Overall design: Using RPA ChIP-seq in cytokine-activated B cells to identified recurrent, unidirectional DSBs in rDNA region.