Project description: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.
Project description:We report the effect of degradation of CEBPA (a critical myeloid lineage transcription factor) on the occupancy of core rRNA transcription machinery on rDNA in mouse GMP cells. We generated a CEBPA-Degron line by tagging endogenous alleles of the Cebpa gene with the FKBPV degron domain, and degraded CEBPA-FKBPV-FLAG fusion protein using dTAGV-1 ligand. We used anti-FLAG pulldown to demonstrate binding of CEBPA protein to rDNA at a conserved motif within the 18S transcribed region. On degradation of CEBPA, we found that RPA194 (component of Pol I) and RRN3 occupancy on rDNA were reduced, while the occupancy of upstream factors TAF1B (component of SL-1) and UBTF were unchanged. In parallel, we also found that CEBPA degradation reduced nascent rRNA transcription, cellular ribosome abundance, and cell growth. Our work indicates that the cell-type-specific transcription factor CEBPA recruits the Pol I-RRN3 complex to ribosomal DNA to promote rRNA transcription.
2022-01-15 | GSE193569 | GEO
Project description:18s rDNA gene diversity1
| PRJNA719545 | ENA
Project description:phytoplankton community 18S rDNA