Impact of circadian rhythm on DNA methylation in Arabidopsis

Circadian clock is a conserved molecular mechanism required for diurnal transcriptional control of endogenous genes that govern organismal adaptation to environmental light conditions. However, diurnal control of epigenetic modifications, and the impact of the circadian clock on epigenome coordination in plant genomes, remain largely unexplored. To investigate the impact of diurnal day/night cycles on DNA methylation profiles in Arabidopsis, we performed genome-wide analysis of DNA methylation for 24 hr under a long-day, as well as continuous light conditions. The results show that DNA methylation is stably maintained throughout the diurnal cycle, and is also robust to continuous light in wild-type plants. However, loss of the circadian clock in mutants of pseudo-response regulator 9/7/5 (d975) and circadian clock-associated 1/late elongated hypocotyl (cca1 lhy), results in induction of numerous Differentially Methylated Regions (DMRs) throughout the genome. Moreover, changes in DNA methylation were accompanied misregulation of DNA methyltransferase genes. Our study reveals the importance of the circadian clock for homeostasis of global DNA methylation in the Arabidopsis genome.