Methylation of the ribosomal RNA gene promoter is associated with aging and age-related decline

Abstract

The transcription of ribosomal RNA genes (rDNA) is subject to epigenetic regulation, as it is abrogated by the methylation of CpG dinucleotides within their promoter region. Here, we investigated, through Sequenom platform, the age-related methylation status of the CpG island falling into the rDNA promoter in 472 blood samples from 20- to 105-year-old humans and in different tissues (blood, heart, liver, kidney, and testis) of 15 rats 3-96 weeks old. In humans, we did not find a consistently significant correlation between CpG site methylation and chronological age. Furthermore, the methylation levels of one of the analyzed CpG sites were negatively associated with both cognitive performance and survival chance measured in a 9-year follow-up study. We consistently confirmed such result in a replication sample. In rats, the analysis of the homologous region in the tissues revealed the existence of increased methylation in old rats. rRNA expression data, in both humans and rats, were consistent with observed methylation patterns, with a lower expression of rRNA in highly methylated samples. As chronological and biological ages in rats of a given strain are likely to be much closer to each other than in humans, these results seem to provide the first evidence that epigenetic modifications of rDNA change over time according to the aging decline. Thus, the methylation profile of rDNA may represent a potential biomarker of aging.

Keywords: aging; biological age; chronological age; geriatric parameters; ribosomal DNA (rDNA) promoter; ribosomal RNA (rRNA) genes.

Figure 1

Scatter plot of DNA methylation values as a function of human age. For each CpG unit, the red straight line represents least‐squares linear regression line.

Figure 2

Kaplan–Meier survival curves of human samples stratified according to CpG_5 methylation status of samples belonging to the discovery (A) and replication (B) datasets. Solid line represents the subgroup of subjects with a methylation level higher than 20%; dashed line represents the subgroup with a methylation level lower than (or equal to) 20%.

Figure 3

Scatter plot of DNA methylation values as a function of age in rats. For each CpG unit and tissue, the red straight line represents least‐squares linear regression line. Values are reported as the mean of three independent triplicate experiments carried out for each time point.

Figure 4

Expression levels of rDNA measured in human blood (A) and heart, liver, kidney, and testis from rats (B) of different aged. These levels are reported as the mean of relative quantification values (RQ), measured in three independent triplicate experiments with standard error mean (SEM).