Abstract: Background: Age-associated changes in genomic DNA methylation have been primarily attributed to 5-methylcytosine
(5mC). However, the recent discovery of 5-hydroxymethylcytosine (5hmC) suggests that this epigenetic mark
might also play a role in the process.
Methods: Here, we analyzed the genome-wide profile of 5hmc in mesenchymal stem cells (MSCs) obtained from
bone-marrow donors, aged 2–89 years.
Results: We identified 10,685 frequently hydroxymethylated CpG sites in MSCs that were, as in other cell types, significantly
associated with low density CpG regions, introns, the histone posttranslational modification H3k4me1 and
enhancers. Study of the age-associated changes to 5hmC identified 785 hyper- and 846 hypo-hydroxymethylated
CpG sites in the MSCs obtained from older individuals.
Conclusions: DNA hyper-hydroxymethylation in the advanced-age group was associated with loss of 5mC, which
suggests that, at specific CpG sites, this epigenetic modification might play a role in DNA methylation changes during
lifetime. Since bone-marrow MSCs have many clinical applications, and the fact that the epigenomic alterations in
this cell type associated with aging identified in this study could have associated functional effects, the age of donors
should be taken into account in clinical settings.