Abstract

The circadian clock acts at the genomic level to coordinate internal behavioural and physiological rhythms via the CLOCK–BMAL1 transcriptional heterodimer. Although the nuclear receptors REV-ERB-α and REV-ERB-β have been proposed to form an accessory feedback loop that contributes to clock function1,2, their precise roles and importance remain unresolved. To establish their regulatory potential, we determined the genome-wide cis-acting targets (cistromes) of both REV-ERB isoforms in murine liver, which revealed shared recognition at over 50% of their total DNA binding sites and extensive overlap with the master circadian regulator BMAL1. Although REV-ERB-α has been shown to regulate Bmal1 expression directly1,2, our cistromic analysis reveals a more profound connection between BMAL1 and the REV-ERB-α and REV-ERB-β genomic regulatory circuits than was previously suspected. Genes within the intersection of the BMAL1, REV-ERB-α and REV-ERB-β cistromes are highly enriched for both clock and metabolic functions. As predicted by the cistromic analysis, dual depletion of Rev-erb-α and Rev-erb-β function by creating double-knockout mice profoundly disrupted circadian expression of core circadian clock and lipid homeostatic gene networks. As a result, double-knockout mice show markedly altered circadian wheel-running behaviour and deregulated lipid metabolism. These data now unite REV-ERB-α and REV-ERB-β with PER, CRY and other components of the principal feedback loop that drives circadian expression and indicate a more integral mechanism for the coordination of circadian rhythm and metabolism.

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Accessions

Primary accessions

Gene Expression Omnibus

Data deposits

Microarray and ChIP-seq data sets have been deposited in the NCBI Gene Expression Omnibus with the accession number GSE34020.

References

  1. 1.

    et al. The orphan nuclear receptor REV-ERBα controls circadian transcription within the positive limb of the mammalian circadian oscillator. Cell 110, 251–260 (2002)

  2. 2.

    et al. Redundant function of REV-ERBα and β and non-essential role for Bmal1 cycling in transcriptional regulation of intracellular circadian rhythms. PLoS Genet. 4, e1000023 (2008)

  3. 3.

    et al. Role of the CLOCK protein in the mammalian circadian mechanism. Science 280, 1564–1569 (1998)

  4. 4.

    , & CLOCK and NPAS2 have overlapping roles in the suprachiasmatic circadian clock. Nature Neurosci. 10, 543–545 (2007)

  5. 5.

    et al. Nonredundant roles of the mPer1 and mPer2 genes in the mammalian circadian clock. Cell 105, 683–694 (2001)

  6. 6.

    et al. Mammalian Cry1 and Cry2 are essential for maintenance of circadian rhythms. Nature 398, 627–630 (1999)

  7. 7.

    et al. Differential regulation of mammalian period genes and circadian rhythmicity by cryptochromes 1 and 2. Proc. Natl Acad. Sci. USA 96, 12114–12119 (1999)

  8. 8.

    & Circadian rhythms: mechanisms and therapeutic implications. Annu. Rev. Pharmacol. Toxicol. 47, 593–628 (2007)

  9. 9.

    et al. Delay in feedback repression by cryptochrome 1 is required for circadian clock function. Cell 144, 268–281 (2011)

  10. 10.

    et al. Nuclear receptor expression links the circadian clock to metabolism. Cell 126, 801–810 (2006)

  11. 11.

    et al. A circadian rhythm orchestrated by histone deacetylase 3 controls hepatic lipid metabolism. Science 331, 1315–1319 (2011)

  12. 12.

    et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl Acad. Sci. USA 102, 15545–15550 (2005)

  13. 13.

    et al. REV-ERBα participates in circadian SREBP signaling and bile acid homeostasis. PLoS Biol. 7, e1000181 (2009)

  14. 14.

    et al. Genome-wide and phase-specific DNA-binding rhythms of BMAL1 control circadian output functions in mouse liver. PLoS Biol. 9, e1000595 (2011)

  15. 15.

    et al. Increased cell death and delayed development in the cerebellum of mice lacking the rev-erbAα orphan receptor. Development 127, 1489–1498 (2000)

  16. 16.

    et al. Dual roles for glucokinase in glucose homeostasis as determined by liver and pancreatic beta cell-specific gene knock-outs using Cre recombinase. J. Biol. Chem. 274, 305–315 (1999)

  17. 17.

    , , & Transcriptional profiling in the adrenal gland reveals circadian regulation of hormone biosynthesis genes and nucleosome assembly genes. J. Biol. Rhythms 21, 350–361 (2006)

  18. 18.

    et al. Circadian and CLOCK-controlled regulation of the mouse transcriptome and cell proliferation. Proc. Natl Acad. Sci. USA 104, 3342–3347 (2007)

  19. 19.

    et al. Genome-wide profiling of the core clock protein BMAL1 targets reveals a strict relationship with metabolism. Mol. Cell. Biol. 30, 5636–5648 (2010)

  20. 20.

    et al. System-driven and oscillator-dependent circadian transcription in mice with a conditionally active liver clock. PLoS Biol. 5, e34 (2007)

  21. 21.

    & Efficient recombination in diverse tissues by a tamoxifen-inducible form of Cre: a tool for temporally regulated gene activation/inactivation in the mouse. Dev. Biol. 244, 305–318 (2002)

  22. 22.

    et al. Mop3 is an essential component of the master circadian pacemaker in mammals. Cell 103, 1009–1017 (2000)

  23. 23.

    et al. Circadian rhythms, sleep, and metabolism. J. Clin. Invest. 121, 2133–2141 (2011)

  24. 24.

    et al. Identification of Rev-erbα as a physiological repressor of apoC-III gene transcription. J. Lipid Res. 43, 2172–2179 (2002)

  25. 25.

    et al. Regulation of adipogenesis by natural and synthetic REV-ERB ligands. Endocrinology 151, 3015–3025 (2010)

  26. 26.

    et al. The nuclear receptor REV-ERBα mediates circadian regulation of innate immunity through selective regulation of inflammatory cytokines. Proc. Natl Acad. Sci. USA 109, 582–587 (2012)

  27. 27.

    , , & Circadian rhythms, sleep, and metabolism. J. Clin. Invest. 121, 2133–2141 (2011)

  28. 28.

    et al. AMPK regulates the circadian clock by cryptochrome phosphorylation and degradation. Science 326, 437–440 (2009)

  29. 29.

    et al. Cryptochromes mediate rhythmic repression of the glucocorticoid receptor. Nature 480, 552–556 (2011)

  30. 30.

    , , & Identification of SR8278, a synthetic antagonist of the nuclear heme receptor REV-ERB. ACS Chem. Biol. 6, 131–134 (2011)

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Acknowledgements

We thank S. Kaufman, J. Alvarez, E. Banayo, H. Juguilon, S. Jacinto and H. Le for technical assistance; and L. Ong and S. Ganley for administrative assistance. We also thank L. Pei for discussion. R.M.E is an Investigator of the Howard Hughes Medical Institute at The Salk Institute for Biological Studies and March of Dimes Chair in Molecular and Developmental Biology. H.C. is a recipient of National Research Service Award (T32-HL007770). This work was supported by National Institutes of Health Grants (DK062434, DK057978, DK090962, DK091618 and HL105278), National Health and Medical Research Council of Australia Project Grants (NHMRC 512354 and 632886), the Helmsley Charitable Trust, the Glenn Foundation and the Howard Hughes Medical Institute.

Author information

Affiliations

  1. Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, California 92037, USA

    • Han Cho
    • , Xuan Zhao
    • , Ruth T. Yu
    • , Grant D. Barish
    • , Ling-Wa Chong
    • , Annette R. Atkins
    • , Michael Downes
    •  & Ronald M. Evans
  2. Regulatory Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California 92037, USA

    • Megumi Hatori
    • , Luciano DiTacchio
    •  & Satchidananda Panda
  3. Department of Cellular and Molecular Medicine, School of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093-0651, USA

    • Michael T. Lam
    •  & Christopher K. Glass
  4. The Storr Liver Unit, Westmead Millennium Institute and University of Sydney, Westmead Hospital, Westmead, New South Wales 2145, Australia

    • Christopher Liddle
  5. Ecole Polytechnique Fédérale in Lausanne CH-1015, Lausanne, Switzerland

    • Johan Auwerx
  6. Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, California 92037, USA

    • Ronald M. Evans

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Contributions

X.Z., G.D.B., R.T.Y., M.D. and C.L. performed and/or analysed the results from ChIP-seq. R.T.Y., M.D., M.T.L. and C.K.G. performed and/or analysed the results from the microarray experiment. M.H., L.D. and S.P. performed and/or analysed the wheel-running assay and the real-time luciferase assay. J.A. performed gene targeting. H.C. and L.-W.C. performed all experiments. H.C. and R.M.E. designed all experiments, analysed all results and H.C., R.T.Y., M.D., A.R.A., S.P. and R.M.E. wrote the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Ronald M. Evans.

Supplementary information

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    Supplementary Information

    This file contains Supplementary Materials and Methods, Supplementary Figure 1-8 and Supplementary Tables 1-7. This file was replaced on 26 September 2012 to correct errors in Supplementary Figure 4.

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DOI

https://doi.org/10.1038/nature11048

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