Daily rhythm in DNA methylation and the effect of total sleep deprivation

Numerous hormones and genes exhibit diurnal 24-hr rhythms that can also be affected by sleep deprivation. Here we studied diurnal rhythms in DNA methylation under a 24-hr sleep/wake cycle and a subsequent 29 hr of continual wakefulness (1 night of sleep deprivation). Fifteen healthy men (19-35 years) spent 3 days/nights in a sleep laboratory: (1) adaptation; (2) baseline; (3) total sleep deprivation day/night. DNA methylation was analysed from peripheral blood leukocytes, collected every 3 hr for 45 hr (starting at 15:00 hours) during the baseline period and the total sleep deprivation period. Epigenome-wide DNA methylation variation was assessed with the Infinium MethylationEPIC v2.0 Beadchip kit. Rhythm analysis was performed separately for the baseline and the total sleep deprivation time-series data. Pairwise analysis between diurnal samples and sleep deprivation samples at the same timepoint was also carried out to detect differentially methylated positions related to sleep deprivation. Of all DNA methylation sites, 14% exhibited a diurnal rhythm in methylation on the baseline day/night that was altered by sleep deprivation. During sleep deprivation, the number of differentially methylated positions increased towards the end of the sleep deprivation period, with a dominating pattern of hypomethylation. Among differentially methylated positions, an enrichment of genes related to the FAS immune response pathway was detected. In conclusion, DNA methylation exhibits diurnal rhythmicity, and this time-of-day variation needs to be considered when studying DNA methylation as a biomarker in biomedical studies. In addition, the observed DNA methylation changes under wakefulness might serve as a mediator of sleep deprivation-related immune response alterations.