Aging and DNA methylation in Alu and LINE-1 repeated elements

DNA methylation exhibits a gradual genome-wide decrease in association with aging and the rate of decrease appears to be inversely proportional to life expectancy. The observed age-related increase in cancer incidence cannot be explained entirely by genetic mutation rates. Accumulation of epigenetic alterations during aging may contribute to determine the malignant transformation. In particular, global DNA hypomethylation, which has been associated with repetitive DNA demethylation may promote chromosomal instability. About 55% of the human genome consists of repetitive elements, which are for the most part made up of approximately 500,000 long interspersed nucleotide elements (LINE elements) and 1.4 million Alu repetitive elements, which are normally heavily methylated. DNA methylation of LINE-1 and Alu elements has shown to correlate with total 5mC content and thus used to estimate global DNA methylation. In humans, LINEs are the major source of insertional mutagenesis, being involved in both germinal and somatic mutant phenotypes. Alu retrotransposition has also been associated with human disease. However, whether LINE/Alu methylation decreases with age has never been established. We examined the epigenetic effect of aging on DNA methylation in repetitive elements Alu and LINE-1, measured in peripheral blood DNA from 693 subjects evaluated between 1999-2006 as part of the Normative Aging Study (NAS), a longitudinal study established in 1963 by the U.S. Veterans Administration. We measured DNA methylation through quantitative analysis by PCR-Pyrosequencing. Two different blood samples, taken approximately three years apart, were available for each subject. Repeated element methylation was negatively associated with age. In linear regression, we found a decrease equal to 0.016% for LINE-1 (p=0.07) and 0.015% for Alu (p=0.007), for each year increase. We did not find significant changes between repeated measures taken three years apart from each other on the same subjects. The two repeated measures showed high correlation for both Alu (n=300, r=0.46, p<0.001) for Alu and LINE-1 (n=303, r=0.59, p<0.001). DNA methylation of LINE-1 and Alu repetitive elements is inversely correlated with age, although is not captured in repeated measurements taken over a three years period. Such age-related decrease in methylation may increase the risk of mutational events potentially leading to cancer development.