rDNA Copy Number Variation and Methylation During Normal and Premature Aging

Ribosomal RNA is the main component of the ribosome, which is essential for protein synthesis. The diploid human genome contains several hundred copies of the rDNA transcription unit (TU). Droplet digital PCR and deep bisulfite sequencing were used to determine the absolute copy number (CN) and the methylation status of individual rDNA TU in blood samples of healthy individuals. The absolute CN ranged from 243 to 895 (median 469). There was no difference in absolute CN between males and females and no gain or loss of copies with age (15–71 years). The number of rDNA TU with a completely unmethylated (0%) or lowly methylated (1%–10%) promoter region significantly decreased, whereas the number of copies with higher (11%–100%) methylation increased with age. The number of presumably active TU with a hypomethylated (0%–10%) promoter varied from 94 to 277 (median 180), independent from absolute CN. In contrast, the number of inactive hypermethylated (11%–100%) copies strongly increased with absolute CN. Promoter hypermethylation compensates to some extent for the enormous CN variation among individuals. Patients with Werner syndrome, a premature aging syndrome displayed the same CN variation and age-related methylation changes as controls. The role of rDNA CN variation as a modulating factor in human health and disease is largely unexplored. In particular, very low and high CN may be associated with increased disease risk.