Age-dependent patterns of X chromosome DNA methylation in the elderly.

The age-dependent patterns of DNA methylation in the elderly population have been intensively studied on the autosomal chromosomes, revealing large numbers of genomic sites under significant epigenetic remodeling during the aging process. However, DNA methylation changes on the X-chromosomes have been routinely ignored due to analytical difficulties in dealing with difference in X chromosome content of females and males and X chromosome inactivation in females. Taking advantage of large sample sizes of DNA methylation data available on the elderly, we performed X-chromosome-wide association study on X-linked DNA methylation changes during aging by analyzing male and female samples separately and comparing the rate of change in DNA methylation between sexes to identify significant CpGs sites differentially or consistently methylated in males and females. We detected 2300 significant CpGs (False Discovery Rate<0.05) displaying sex-independent methylation patterns and 286 CpGs showing sex-dependent methylation changes in the Lothian birth cohort born in 1936 in Scotland (732 males with mean age 71.27 and 732 females with mean age 71.23). As a replication approach, a similar analysis was performed in an independent sample of middle aged Danish twins (226 males with mean age 67.26 and 226 females with mean age 66.04) reporting 136 CpGs consistently and 59 CpGs differentially methylated in males and females with overlapping rates of 38.08% and 5.1% with the discovery results. In conclusion, we have shown significant DNA methylation patterns of aging on the X-chromosome dominated by sex-independent regulation highly replicable in independent samples.