Age-Dependent Ribosomal DNA Variations in Mice

Abstract

The rRNA gene, which consists of tandem repetitive arrays (ribosomal DNA [rDNA] repeat), is one of the most unstable regions in the genome. The rDNA repeat in the budding yeast Saccharomyces cerevisiae is known to become unstable as the cell ages. However, it is unclear how the rDNA repeat changes in aging mammalian cells. Using quantitative single-cell analyses, we identified age-dependent alterations in rDNA copy number and levels of methylation in mice. The degree of methylation and copy number of rDNA from bone marrow cells of 2-year-old mice were increased by comparison to levels in 4-week-old mice in two mouse strains, BALB/cA and C57BL/6. Moreover, the level of pre-rRNA transcripts was reduced in older BALB/cA mice. We also identified many sequence variations in the rDNA. Among them, three mutations were unique to old mice, and two of them were found in the conserved region in budding yeast. We established yeast strains with the old-mouse-specific mutations and found that they shortened the life span of the cells. Our findings suggest that rDNA is also fragile in mammalian cells and that alterations within this region have a profound effect on cellular function.

Thousands of high-quality sequencing samples fail to show meaningful correlation between 5S and 45S ribosomal DNA arrays in humans

“…However, one study argues that rDNA instability is only observed in brains of individuals affected by dementia, and is absent in aging brains of healthy individuals 12 . In contrast, a recent study on aging mice found that 45S rDNA copy number increases in the blood with age in mice 13 . Additional studies in mice and rat cell lines report a lack of change in rDNA copy number with age [14][15][16] .…”

“…A subset of these findings rely on rDNA copy number estimates from short read sequencing data 1 , 8 , 23 . However, even studies that develop their own rDNA copy number estimation methods still compare to short read sequencing data to comment on their accuracy 4 , 13 . Some of these findings may need to be re-evaluated by applying multiple data quality metrics to the analyzed sequence data, by conducting uniform, high-coverage re-sequencing, or by validating rDNA copy number through alternative approaches.…”

The human ribosomal DNA array is composed of highly homogenized tandem clusters

“…It has been proposed that the rate of methylation of 45S rDNAs is increased with age (Watada et al 2020;Wang and Lemos 2019). We therefore tested this relationship using the two young samples and two older samples obtained by Oxford Nanopore sequencing.…”

Ribosome dysfunction in osteoarthritis

“…The 5S rRNA is transcribed separately in the nucleus by RNA polymerase III and imported in the nucleolus to be integrated into the ribosome biogenesis pathway. In ageing (a major risk factor for osteoarthritis), mouse bone marrow cells have been shown to have an increased rDNA copy number [ 11 ]. However, these rDNA copies have increased CpG methylation levels [ 11 , 12 ], probably leading to the observed reduction of rRNA expression [ 11 ].…”

“…In ageing (a major risk factor for osteoarthritis), mouse bone marrow cells have been shown to have an increased rDNA copy number [ 11 ]. However, these rDNA copies have increased CpG methylation levels [ 11 , 12 ], probably leading to the observed reduction of rRNA expression [ 11 ]. Recent work demonstrated regulation of rRNA expression by a Chromobox 4 (CBX4)-dependent mechanism.…”