Genome wide changes in DNA methylation mark the changing seasons in mammalian calendar cells

The circannual clock drives yearly rhythms, in both plants and animals, to meet the challenges of a changing seasonal environment. The hypothesis that coincidence between photoperiod and the circadian clock acts as a zeitgeber to the circannual clock was originally stated by Bünning’s in 1960, however the precise mechanism by which this occurs is still an unknown. An excellent candidate for the location of a circannual clock is the pars tuberalis: a region at the neck of the pituitary with a high concentration of melatonin receptors. We have previously shown (Cur Bio, 2015) that cells in the PT demonstrate binary switching of states between long (LP) and short photoperiods (SP). Epigenetics is an obvious contender for marking the accumulative history of coincidence between circadian clock and melatonin, similar to the established vernalisation process in plants.
We measured genome wide changes in DNA methylation in the ovine pars tuberalis (PT) by RRBS. We sampled two 24hr time series at 4 weeks of SP and LP, together with samples taken at the inductive and refractory phases (confirmed with PRL assays). Parallel RNASeq was done on the same tissue. CAGE and H3K4me3 ChIPSeq provided identification of active promoter regions, which enable us to correlate promoter and gene-body CpG sites to transcript changes.
Significant changes in CpG methylation were observed between photoperiods. We confirmed a negative correlation to transcript levels for CpG methylation at the promoters, and a positive correlation at the gene body. Although this proved to be a general trend rather than a rule, which reflects the complexity of the interactions between the epigenome and transcriptome.
We concluded that there are photoperiod dependent changes in DNA methylation, which may have a role in marking the history of photoperiod in the PT. Work is ongoing to elucidate how specific sites of CpG methylation fit into our current models for the circannual clockwork.