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Circadian behavior is light-reprogrammed by plastic DNA methylation

Abstract

The timing of daily circadian behavior can be highly variable among different individuals, and twin studies have suggested that about half of this variability is environmentally controlled. Similar plasticity can be seen in mice exposed to an altered lighting environment, for example, 22-h instead of 24-h, which stably alters the genetically determined period of circadian behavior for months. The mechanisms mediating these environmental influences are unknown. We found that transient exposure of mice to such lighting stably altered global transcription in the suprachiasmatic nucleus (SCN) of the hypothalamus (the master clock tissue regulating circadian behavior in mammals). In parallel, genome-wide methylation profiling revealed global alterations in promoter DNA methylation in the SCN that correlated with these changes. Behavioral, transcriptional and DNA methylation changes were reversible after prolonged re-entrainment to 24-h d. Notably, infusion of a methyltransferase inhibitor to the SCN suppressed period changes. We conclude that the SCN utilizes DNA methylation as a mechanism to drive circadian clock plasticity.

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Figure 1: Altered day length in young mice alters the FRP and gene expression in the SCN.
Figure 2: The SCN global transcriptome is altered by day length.
Figure 3: Chromatin-modifying enzymes, histone methyltransferases and their regulators show altered expression during aftereffects of T-cycle exposure.
Figure 4: Altered day length induces global changes in DNA methylation in the SCN.
Figure 5: Zebularine suppresses period length changes during entrainment to altered day lengths.
Figure 6: DNMT3a protein expression decreases with aging.

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References

  1. Dibner, C., Schibler, U. & Albrecht, U. The mammalian circadian timing system: organization and coordination of central and peripheral clocks. Annu. Rev. Physiol. 72, 517–549 (2010).

    Article  CAS  Google Scholar 

  2. Brown, S.A. et al. The period length of fibroblast circadian gene expression varies widely among human individuals. PLoS Biol. 3, e338 (2005).

    Article  Google Scholar 

  3. Brown, S.A. et al. Molecular insights into human daily behavior. Proc. Natl. Acad. Sci. USA 105, 1602–1607 (2008).

    Article  CAS  Google Scholar 

  4. Barclay, N.L., Eley, T.C., Buysse, D.J., Archer, S.N. & Gregory, A.M. Diurnal preference and sleep quality: same genes? A study of young adult twins. Chronobiol. Int. 27, 278–296 (2010).

    Article  CAS  Google Scholar 

  5. Hur, Y.M. Stability of genetic influence on morningness-eveningness: a cross-sectional examination of South Korean twins from preadolescence to young adulthood. J. Sleep Res. 16, 17–23 (2007).

    Article  Google Scholar 

  6. Koskenvuo, M., Hublin, C., Partinen, M., Heikkila, K. & Kaprio, J. Heritability of diurnal type: a nationwide study of 8753 adult twin pairs. J. Sleep Res. 16, 156–162 (2007).

    Article  Google Scholar 

  7. Pittendrigh, C.S. & Daan, S. A functional analysis of circadian pacemakers in nocturnal rodents. J. Comp. Physiol. 106, 223–252 (1976).

    Article  Google Scholar 

  8. Chang, A.M., Scheer, F.A. & Czeisler, C.A. The human circadian system adapts to prior photic history. J. Physiol. (Lond.) 589, 1095–1102 (2011).

    Article  CAS  Google Scholar 

  9. LeGates, T.A. et al. Aberrant light directly impairs mood and learning through melanopsin-expressing neurons. Nature 491, 594–598 (2012).

    Article  CAS  Google Scholar 

  10. Bird, A. DNA methylation patterns and epigenetic memory. Genes Dev. 16, 6–21 (2002).

    Article  CAS  Google Scholar 

  11. Guo, J.U. et al. Neuronal activity modifies the DNA methylation landscape in the adult brain. Nat. Neurosci. 14, 1345–1351 (2011).

    Article  CAS  Google Scholar 

  12. Murgatroyd, C. et al. Dynamic DNA methylation programs persistent adverse effects of early-life stress. Nat. Neurosci. 12, 1559–1566 (2009).

    Article  CAS  Google Scholar 

  13. Day, J.J. & Sweatt, J.D. DNA methylation and memory formation. Nat. Neurosci. 13, 1319–1323 (2010).

    Article  CAS  Google Scholar 

  14. Ball, M.P. et al. Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells. Nat. Biotechnol. 27, 361–368 (2009).

    Article  CAS  Google Scholar 

  15. Molyneux, P.C., Dahlgren, M.K. & Harrington, M.E. Circadian entrainment aftereffects in suprachiasmatic nuclei and peripheral tissues in vitro. Brain Res. 1228, 127–134 (2008).

    Article  CAS  Google Scholar 

  16. Stevenson, T.J. & Prendergast, B.J. Reversible DNA methylation regulates seasonal photoperiodic time measurement. Proc. Natl. Acad. Sci. USA 110, 16651–16656 (2013).

    Article  CAS  Google Scholar 

  17. Huang, D.W., Sherman, B.T. & Lempicki, R.A. Systematic and integrative analysis of large gene lists using DAVID Bioinformatics Resources. Nat. Protoc. 4, 44–57 (2009).

    Article  CAS  Google Scholar 

  18. Masri, S. & Sassone-Corsi, P. The circadian clock: a framework linking metabolism, epigenetics and neuronal function. Nat. Rev. Neurosci. 14, 69–75 (2013).

    Article  CAS  Google Scholar 

  19. Franchini, D.M., Schmitz, K.M. & Petersen-Mahrt, S.K. 5-Methylcytosine DNA demethylation: more than losing a methyl group. Annu. Rev. Genet. 46, 419–441 (2012).

    Article  CAS  Google Scholar 

  20. Miller, C.A. et al. Cortical DNA methylation maintains remote memory. Nat. Neurosci. 13, 664–666 (2010).

    Article  CAS  Google Scholar 

  21. Vollmers, C. et al. Circadian oscillations of protein-coding and regulatory RNAs in a highly dynamic mammalian liver epigenome. Cell Metab. 16, 833–845 (2012).

    Article  CAS  Google Scholar 

  22. Miller, C.A. & Sweatt, J.D. Covalent modification of DNA regulates memory formation. Neuron 53, 857–869 (2007).

    Article  CAS  Google Scholar 

  23. Champion, C. et al. Mechanistic insights on the inhibition of c5 DNA methyltransferases by zebularine. PLoS ONE 5, e12388 (2010).

    Article  Google Scholar 

  24. Belden, W.J., Lewis, Z.A., Selker, E.U., Loros, J.J. & Dunlap, J.C. CHD1 remodels chromatin and influences transient DNA methylation at the clock gene frequency. PLoS Genet. 7, e1002166 (2011).

    Article  CAS  Google Scholar 

  25. Ciarleglio, C.M., Axley, J.C., Strauss, B.R., Gamble, K.L. & McMahon, D.G. Perinatal photoperiod imprints the circadian clock. Nat. Neurosci. 14, 25–27 (2011).

    Article  CAS  Google Scholar 

  26. Zhang, L. et al. Tissue-specific modification of clock methylation in aging mice. Eur. Rev. Med. Pharmacol. Sci. 17, 1874–1880 (2013).

    CAS  PubMed  Google Scholar 

  27. Shi, F. et al. Aberrant DNA methylation of miR-219 promoter in long-term night shiftworkers. Environ. Mol. Mutagen. 54, 406–413 (2013).

    Article  CAS  Google Scholar 

  28. Zhu, Y. et al. Epigenetic impact of long-term shiftwork: pilot evidence from circadian genes and whole-genome methylation analysis. Chronobiol. Int. 28, 852–861 (2011).

    Article  CAS  Google Scholar 

  29. Milagro, F.I. et al. CLOCK, PER2 and BMAL1 DNA methylation: association with obesity and metabolic syndrome characteristics and monounsaturated fat intake. Chronobiol. Int. 29, 1180–1194 (2012).

    Article  CAS  Google Scholar 

  30. Maekawa, F. et al. Diurnal expression of Dnmt3b mRNA in mouse liver is regulated by feeding and hepatic clockwork. Epigenetics 7, 1046–1056 (2012).

    Article  CAS  Google Scholar 

  31. Levenson, J.M. et al. Evidence that DNA (cytosine-5) methyltransferase regulates synaptic plasticity in the hippocampus. J. Biol. Chem. 281, 15763–15773 (2006).

    Article  CAS  Google Scholar 

  32. Ciarleglio, C.M., Axley, J.C., Strauss, B.R., Gamble, K.L. & McMahon, D.G. Perinatal photoperiod imprints the circadian clock. Nat. Neurosci. 14, 25–27 (2011).

    Article  CAS  Google Scholar 

  33. Roenneberg, T. et al. A marker for the end of adolescence. Curr. Biol. 14, R1038–R1039 (2004).

    Article  CAS  Google Scholar 

  34. Pagani, L. et al. Serum factors in older individuals change cellular clock properties. Proc. Natl. Acad. Sci. USA 108, 7218–7223 (2011).

    Article  CAS  Google Scholar 

  35. Kaas, G.A. et al. TET1 controls CNS 5-methylcytosine hydroxylation, active DNA demethylation, gene transcription, and memory formation. Neuron 79, 1086–1093 (2013).

    Article  CAS  Google Scholar 

  36. Rudenko, A. et al. Tet1 is critical for neuronal activity-regulated gene expression and memory extinction. Neuron 79, 1109–1122 (2013).

    Article  CAS  Google Scholar 

  37. Zovkic, I.B., Guzman-Karlsson, M.C. & Sweatt, J.D. Epigenetic regulation of memory formation and maintenance. Learn. Mem. 20, 61–74 (2013).

    Article  CAS  Google Scholar 

  38. Franchini, D.M., Schmitz, K.M. & Petersen-Mahrt, S.K. 5-Methylcytosine DNA demethylation: more than losing a methyl group. Annu. Rev. Genet. 46, 419–441 (2012).

    Article  CAS  Google Scholar 

  39. Lemaire, M., Momparler, L.F., Raynal, N.J., Bernstein, M.L. & Momparler, R.L. Inhibition of cytidine deaminase by zebularine enhances the antineoplastic action of 5-aza-2′-deoxycytidine. Cancer Chemother. Pharmacol. 63, 411–416 (2009).

    Article  CAS  Google Scholar 

  40. Brown, S.A., Zumbrunn, G., Fleury-Olela, F., Preitner, N. & Schibler, U. Rhythms of mammalian body temperature can sustain peripheral circadian clocks. Curr. Biol. 12, 1574–1583 (2002).

    Article  CAS  Google Scholar 

  41. Halbritter, F., Vaidya, H.J. & Tomlinson, S.R. GeneProf: analysis of high-throughput sequencing experiments. Nat. Methods 9, 7–8 (2012).

    Article  CAS  Google Scholar 

  42. Trapnell, C., Pachter, L. & Salzberg, S.L. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25, 1105–1111 (2009).

    Article  CAS  Google Scholar 

  43. Anders, S. & Huber, W. Differential expression analysis for sequence count data. Genome Biol. 11, R106 (2010).

    Article  CAS  Google Scholar 

  44. Weber, M. et al. Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells. Nat. Genet. 37, 853–862 (2005).

    Article  CAS  Google Scholar 

  45. Rai, K. et al. DNA demethylase activity maintains intestinal cells in an undifferentiated state following loss of APC. Cell 142, 930–942 (2010).

    Article  CAS  Google Scholar 

  46. Song, J.S. et al. Model-based analysis of two-color arrays (MA2C). Genome Biol. 8, R178 (2007).

    Article  Google Scholar 

  47. Kramer, A. et al. Regulation of daily locomotor activity and sleep by hypothalamic EGF receptor signaling. Science 294, 2511–2515 (2001).

    Article  CAS  Google Scholar 

  48. DeBruyne, J.P., Weaver, D.R. & Reppert, S.M. CLOCK and NPAS2 have overlapping roles in the suprachiasmatic circadian clock. Nat. Neurosci. 10, 543–545 (2007).

    Article  CAS  Google Scholar 

  49. Kowalska, E. et al. Distinct roles of DBHS family members in the circadian transcriptional feedback loop. Mol. Cell. Biol. 32, 4585–4594 (2012).

    Article  CAS  Google Scholar 

  50. Oakes, C.C., La Salle, S., Robaire, B. & Trasler, J.M. Evaluation of a quantitative DNA methylation analysis technique using methylation-sensitive/dependent restriction enzymes and real-time PCR. Epigenetics 1, 146–152 (2006).

    Article  Google Scholar 

  51. Maier, B. et al. A large-scale functional RNAi screen reveals a role for CK2 in the mammalian circadian clock. Genes Dev. 23, 708–718 (2009).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

This work was supported by the Velux Foundation, the Swiss National Science Foundation and the Zürich Clinical Research Program 'Sleep and Health'. A.A. and S.A.B. are members of the Zürich Neurozentrum graduate program, and S.A.B. is also a member of the Molecular Life Sciences program. R.D. is a Feodor Lynen Fellow of the Humboldt Foundation.

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A.A. and A.C. performed all experiments, with assistance from R.D., H.R. and A.P. Knockdown experiments in U2OS cells were performed and analyzed by B.M. with assistance from A.K. Data analysis was conducted by A.A., R.D., H.R., B.M. and A.P. The paper was written by A.A., R.D., B.M., A.K. and S.A.B.

Corresponding author

Correspondence to Steven A Brown.

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The authors declare no competing financial interests.

Integrated supplementary information

Supplementary Figure 1 Basic experimental design used to test for aftereffects.

All mice were raised under normal day lengths of 24 hours during the first four weeks after birth. They were then transferred to individual cages and exposed to constant darkness (DD) for 7 days to record their free running period (FRP). After 7 days they received an additional 6 weeks of altered environment — exposed to short day length (ST) (Light:Dark 11:11), normal day length (NT) (L:D: 12:12), or long day length (LT) (L:D 13:13). After entrainment, all mice were then transferred to DD for an additional 10 days to record their FRP.

Supplementary Figure 2 Entrainment to different day lengths (T-cycles) is stable for months in constant conditions.

Representative double-plotted actograms of mice entrained to ST and LT. Four-week-old mice were exposed to DD for 6 days to record their FRP, then entrained to ST and NT-cycles (22 hours or 26 hours) for 4 weeks, and released into DD conditions for 2 months.

Supplementary Figure 3 Old mice neither entrained to short-day ST cycles nor showed aftereffects.

Wheel running behavior assay of mice before, during and after entrainment to ST cycles. Three-week-old mice and 9-month-old mice were exposed to DD for 7 days and then they were entrained to 11:11hours light:dark for 1 month. After entrainment they were exposed to DD during 10 days. (a–b) Representative actograms of (a) young and (b) old mice. (c) average FRP before and after entrainment to ST cycle of old mice (n = 9 mice/group, p = 0.8072, mean ±s.e.m. shown).

Supplementary Figure 4 Circadian clock entrainment is necessary for aftereffects.

Wheel running behavior of mice before, during and after entrainment to LD 11:11 or 10:10. Representative actograms of 4-week-old mice (a, b) exposed to DD for 7 days and then entrained to LD 11:11 or 10:10 LD cycles for 3 weeks. Whereas 11:11 mice could entrain to the assigned photoperiod, 10:10 mice could not. After entrainment, mice were released into DD for 7 days. (c) Average FRP before and after entrainment (n = 5 mice per group, t-test LD 11:11 ** p = 0.0010 and LD 10:10 p = 0.6062, mean ±s.e.m. shown).

Supplementary Figure 5 Clock gene expression during aftereffects of T cycle exposure.

(a and b) Autoradiographs showing coronal brain sections hybridized with circadian gene probes. One month-old mice were entrained to ST and LT cycle for one month and then released into DD. To collect brains at indicated circadian timepoints, FRP was measured after 7 days in DD individually for each mouse. CT0 was defined as one half-cycle after activity onset, and CT12 as activity onset. (c) Quantification of data from mice entrained to ST and LT cycles, and harvested at CT8 (n = 3 mice/group). T-test * p < 0.05, mean ±s.e.m. shown. Quantification of part A is presented in the main text.

Supplementary Figure 6 DNA methylation changes in the SCN require long-term exposure to altered day length.

Methylation levels at Sap30l and Avpr2 promoters for mice entrained to ST and NT for either (a) 2 weeks (2W) or (b) 4 weeks (4W), and then analyzed by methylation-dependent restriction enzyme digestion followed by qPCR. Data are normalized to the maximal methylation observed for each gene. n = 5 mice/group, T-test p< 0.05, mean ±s.e.m. shown.

Supplementary Figure 7 Alterations in methylation observed in the SCN under short T-cycles did not occur in the cortex.

Methylation at the promoters of the E2F8, Golim4, and Vav3 genes in SCN and cortex, determined by MeDIP-qPCR, mean ±s.e.m. shown.

Supplementary Figure 8 Control experiment to demonstrate third ventricle cannulation.

(a) Infusion of TGFα into the third ventricle is known to alter the locomotor activity of mice (Kramer et al., Science (2001) 294:2511-15). Bar graph showing average normalized 3-day activity before, during and after 7 days of infusion with aCSF or TGFα. Four-week-old mice were exposed to DD for 10 days to record their FRP and then infused with aCSF or TGFα for 7 days in DD via osmotic minipump, mean ±s.e.m. shown. (b) Coronal brain section from representative cannulated mice, showing the needle track towards the third ventricle.

Supplementary Figure 9 Infusion of zebularine alone has no effect on the FRP.

(a) Representative actograms of behavioral activity before and during infusion of aCSF or zebularine. (b) Bar graph showing the FRP of mice before and during infusion of aCSF and zebularine in constant darkness. Four-week-old mice were exposed to DD for 10 days to record their FRP and then infused with aCSF or zebularine during 7 days in DD. Red stars indicate the day of pump and cannula implantation. (n = 3 mice per group, no effect of drug in repeated measures ANOVA, p = 0.348, mean ±s.e.m. shown).

Supplementary Figure 10 Experimental design used to examine reversibility of aftereffects.

All mice were raised until 4 weeks of age under a normal light/dark cycle of 24 hours, (NT) (L:D 12:12). They were then transferred to individual cages and exposed to constant darkness (DD) for 7 days to record their free running period (FRP). After 7 days they were exposed for an additional 4 weeks to NT lighting conditions, or exposed to short T (ST) (L:D 11:11). Subsequently, all mice were then transferred to DD for additional 7 days to record their FRP. Finally, all mice from both groups were entrained to NT for 4 weeks, and FRP was recorded under DD conditions.

Supplementary Figure 11 Multiple loci affected by T-cycles are necessary for normal circadian clock function.

Left, Z-scored circadian period of U2OS cells infected with a lentivirus expressing an RNAi hairpin silencing each gene whose transcription was significantly affected by short-day T cycles. Right, Identical graph for genes whose methylation was affected by T cycles. Dotted lines, mean period and its standard deviation.

Supplementary Figure 12 Changes in expression of DNA methyltransferases and tet2–3 enzymes in response to a light pulse.

The bar graph shows the fold changes in transcript levels for the indicated genes following 2 hours of light exposure in mice during the subjective night compared to sham-exposed controls. Six-week-old mice were raised under normal day lengths (NT) and then transferred to constant darkness for two consecutive days. They were then exposed to a 2 hour light pulse (normal room light) or a dark pulse (sham) between circadian time CT12 and CT14. Brains were then collected and sliced immediately to isolate SCNs for RNA analysis. Bars represent mean ±s.e.m. Light pulse vs. sham control unpaired t-test DNMT3a p = 0.011; DNMT3b p = 0.011; Tet2 p = 0.069; Tet3 p = 0.004 Per1 p = 0.002.

Supplementary Figure 13 Single injection of zebularine did not change shortening in FRP after ST cycle entrainment.

(a) Wheel running behavior of mice before, during and after entrainment to ST cycle. At the end of the ST-cycle (4 weeks) mice received a single injection of 500 nl of either aCSF or zebularine (500 uM). Red stars indicate the day of injection. (b) Average FRP before and after entrainment to ST-cycle (n = 4 mice per group, aCSF before vs. after paired t-test ** p = 0.0003, zebularine before vs. after t-test ** p = 0.0005, mean ±s.e.m. shown).

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Azzi, A., Dallmann, R., Casserly, A. et al. Circadian behavior is light-reprogrammed by plastic DNA methylation. Nat Neurosci 17, 377–382 (2014). https://doi.org/10.1038/nn.3651

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