Cycles in spatial and temporal chromosomal organization driven by the circadian clock


Dynamic transitions in the epigenome have been associated with regulated patterns of nuclear organization. The accumulating evidence that chromatin remodeling is implicated in circadian function prompted us to explore whether the clock may control nuclear architecture. We applied the chromosome conformation capture on chip technology in mouse embryonic fibroblasts (MEFs) to demonstrate the presence of circadian long-range interactions using the clock-controlled Dbp gene as bait. The circadian genomic interactions with Dbp were highly specific and were absent in MEFs whose clock was disrupted by ablation of the Bmal1 gene (also called Arntl). We establish that the Dbp circadian interactome contains a wide variety of genes and clock-related DNA elements. These findings reveal a previously unappreciated circadian and clock-dependent shaping of the nuclear landscape.

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Figure 1: Characterization of genomic long-range interactions during the circadian cycle.
Figure 2: Genomic locations of Dbp long-range contacts that follow a BMAL1-dependent circadian pattern of interaction.
Figure 3: FISH validation of 4C data.
Figure 4: Circadian gene expression profiles in DEX-synchronized MEFs.
Figure 5: Circadian expression of Dbp and genes located in spatial proximity.
Figure 6: A schematic model of the cyclic events in chromosomal organization along the circadian cycle.

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  1. 1

    Bass, J. Circadian topology of metabolism. Nature 491, 348–356 (2012).

    CAS  Article  Google Scholar 

  2. 2

    Schibler, U. & Sassone-Corsi, P. A web of circadian pacemakers. Cell 111, 919–922 (2002).

    CAS  Article  Google Scholar 

  3. 3

    Wijnen, H. & Young, M.W. Interplay of circadian clocks and metabolic rhythms. Annu. Rev. Genet. 40, 409–448 (2006).

    CAS  Article  Google Scholar 

  4. 4

    Mohawk, J.A., Green, C.B. & Takahashi, J.S. Central and peripheral circadian clocks in mammals. Annu. Rev. Neurosci. 35, 445–462 (2012).

    CAS  Article  Google Scholar 

  5. 5

    Reppert, S.M. & Weaver, D.R. Coordination of circadian timing in mammals. Nature 418, 935–941 (2002).

    CAS  Article  Google Scholar 

  6. 6

    Doherty, C.J. & Kay, S.A. Circadian control of global gene expression patterns. Annu. Rev. Genet. 44, 419–444 (2010).

    CAS  Article  Google Scholar 

  7. 7

    Aguilar-Arnal, L. & Sassone-Corsi, P. The circadian epigenome: how metabolism talks to chromatin remodeling. Curr. Opin. Cell Biol. 25, 170–176 (2013).

    CAS  Article  Google Scholar 

  8. 8

    Feng, D. & Lazar, M.A. Clocks, metabolism, and the epigenome. Mol. Cell 47, 158–167 (2012).

    CAS  Article  Google Scholar 

  9. 9

    Asher, G. et al. SIRT1 regulates circadian clock gene expression through PER2 deacetylation. Cell 134, 317–328 (2008).

    CAS  Article  Google Scholar 

  10. 10

    DiTacchio, L. et al. Histone lysine demethylase JARID1a activates CLOCK-BMAL1 and influences the circadian clock. Science 333, 1881–1885 (2011).

    CAS  Article  Google Scholar 

  11. 11

    Etchegaray, J.P. et al. The polycomb group protein EZH2 is required for mammalian circadian clock function. J. Biol. Chem. 281, 21209–21215 (2006).

    CAS  Article  Google Scholar 

  12. 12

    Katada, S. & Sassone-Corsi, P. The histone methyltransferase MLL1 permits the oscillation of circadian gene expression. Nat. Struct. Mol. Biol. 17, 1414–1421 (2010).

    CAS  Article  Google Scholar 

  13. 13

    Koike, N. et al. Transcriptional architecture and chromatin landscape of the core circadian clock in mammals. Science 338, 349–354 (2012).

    CAS  Article  Google Scholar 

  14. 14

    Nakahata, Y. et al. The NAD+-dependent deacetylase SIRT1 modulates CLOCK-mediated chromatin remodeling and circadian control. Cell 134, 329–340 (2008).

    CAS  Article  Google Scholar 

  15. 15

    Etchegaray, J.P., Lee, C., Wade, P.A. & Reppert, S.M. Rhythmic histone acetylation underlies transcription in the mammalian circadian clock. Nature 421, 177–182 (2003).

    CAS  Article  Google Scholar 

  16. 16

    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).

    CAS  Article  Google Scholar 

  17. 17

    Le Martelot, G. et al. Genome-wide RNA polymerase II profiles and RNA accumulation reveal kinetics of transcription and associated epigenetic changes during diurnal cycles. PLoS Biol. 10, e1001442 (2012).

    CAS  Article  Google Scholar 

  18. 18

    Hakim, O., Sung, M.H. & Hager, G.L. 3D shortcuts to gene regulation. Curr. Opin. Cell Biol. 22, 305–313 (2010).

    CAS  Article  Google Scholar 

  19. 19

    Rajapakse, I. & Groudine, M. On emerging nuclear order. J. Cell Biol. 192, 711–721 (2011).

    CAS  Article  Google Scholar 

  20. 20

    Sanyal, A., Lajoie, B.R., Jain, G. & Dekker, J. The long-range interaction landscape of gene promoters. Nature 489, 109–113 (2012).

    CAS  Article  Google Scholar 

  21. 21

    Giles, K.E., Gowher, H., Ghirlando, R., Jin, C. & Felsenfeld, G. Chromatin boundaries, insulators, and long-range interactions in the nucleus. Cold Spring Harb. Symp. Quant. Biol. 75, 79–85 (2010).

    CAS  Article  Google Scholar 

  22. 22

    Edelman, L.B. & Fraser, P. Transcription factories: genetic programming in three dimensions. Curr. Opin. Genet. Dev. 22, 110–114 (2012).

    CAS  Article  Google Scholar 

  23. 23

    Sexton, T., Bantignies, F. & Cavalli, G. Genomic interactions: chromatin loops and gene meeting points in transcriptional regulation. Semin. Cell Dev. Biol. 20, 849–855 (2009).

    CAS  Article  Google Scholar 

  24. 24

    Lanctôt, C., Cheutin, T., Cremer, M., Cavalli, G. & Cremer, T. Dynamic genome architecture in the nuclear space: regulation of gene expression in three dimensions. Nat. Rev. Genet. 8, 104–115 (2007).

    Article  Google Scholar 

  25. 25

    Bickmore, W.A. & van Steensel, B. Genome architecture: domain organization of interphase chromosomes. Cell 152, 1270–1284 (2013).

    CAS  Article  Google Scholar 

  26. 26

    Dixon, J.R. et al. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature 485, 376–380 (2012).

    CAS  Article  Google Scholar 

  27. 27

    Lieberman-Aiden, E. et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326, 289–293 (2009).

    CAS  Article  Google Scholar 

  28. 28

    Nora, E.P. et al. Spatial partitioning of the regulatory landscape of the X-inactivation centre. Nature 485, 381–385 (2012).

    CAS  Article  Google Scholar 

  29. 29

    Cavalli, G. & Misteli, T. Functional implications of genome topology. Nat. Struct. Mol. Biol. 20, 290–299 (2013).

    CAS  Article  Google Scholar 

  30. 30

    Ohlsson, R. & Gondor, A. The 4C technique: the 'Rosetta stone' for genome biology in 3D? Curr. Opin. Cell Biol. 19, 321–325 (2007).

    CAS  Article  Google Scholar 

  31. 31

    Simonis, M. et al. Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C). Nat. Genet. 38, 1348–1354 (2006).

    CAS  Article  Google Scholar 

  32. 32

    Ripperger, J.A. & Schibler, U. Rhythmic CLOCK-BMAL1 binding to multiple E-box motifs drives circadian Dbp transcription and chromatin transitions. Nat. Genet. 38, 369–374 (2006).

    CAS  Article  Google Scholar 

  33. 33

    Stratmann, M., Suter, D.M., Molina, N., Naef, F. & Schibler, U. Circadian Dbp transcription relies on highly dynamic BMAL1-CLOCK interaction with E boxes and requires the proteasome. Mol. Cell 48, 277–287 (2012).

    CAS  Article  Google Scholar 

  34. 34

    Wuarin, J. & Schibler, U. Expression of the liver-enriched transcriptional activator protein DBP follows a stringent circadian rhythm. Cell 63, 1257–1266 (1990).

    CAS  Article  Google Scholar 

  35. 35

    Hakim, O. et al. Diverse gene reprogramming events occur in the same spatial clusters of distal regulatory elements. Genome Res. 21, 697–706 (2011).

    CAS  Article  Google Scholar 

  36. 36

    Cremer, T. & Cremer, M. Chromosome territories. Cold Spring Harb. Perspect. Biol. 2, a003889 (2010).

    Article  Google Scholar 

  37. 37

    Zhang, Y. et al. Spatial organization of the mouse genome and its role in recurrent chromosomal translocations. Cell 148, 908–921 (2012).

    CAS  Article  Google Scholar 

  38. 38

    Hakim, O. et al. DNA damage defines sites of recurrent chromosomal translocations in B lymphocytes. Nature 484, 69–74 (2012).

    CAS  Article  Google Scholar 

  39. 39

    Ling, J.Q. et al. CTCF mediates interchromosomal colocalization between Igf2/H19 and Wsb1/Nf1. Science 312, 269–272 (2006).

    CAS  Article  Google Scholar 

  40. 40

    Mahy, N.L., Perry, P.E. & Bickmore, W.A. Gene density and transcription influence the localization of chromatin outside of chromosome territories detectable by FISH. J. Cell Biol. 159, 753–763 (2002).

    CAS  Article  Google Scholar 

  41. 41

    Zhao, Z. et al. Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra- and interchromosomal interactions. Nat. Genet. 38, 1341–1347 (2006).

    CAS  Article  Google Scholar 

  42. 42

    Bian, Q. & Belmont, A.S. Revisiting higher-order and large-scale chromatin organization. Curr. Opin. Cell Biol. 24, 359–366 (2012).

    CAS  Article  Google Scholar 

  43. 43

    Shopland, L.S. et al. Folding and organization of a contiguous chromosome region according to the gene distribution pattern in primary genomic sequence. J. Cell Biol. 174, 27–38 (2006).

    CAS  Article  Google Scholar 

  44. 44

    Schoenfelder, S. et al. Preferential associations between co-regulated genes reveal a transcriptional interactome in erythroid cells. Nat. Genet. 42, 53–61 (2010).

    CAS  Article  Google Scholar 

  45. 45

    Gilbert, N. et al. Chromatin architecture of the human genome: gene-rich domains are enriched in open chromatin fibers. Cell 118, 555–566 (2004).

    CAS  Article  Google Scholar 

  46. 46

    Hogenesch, J.B., Gu, Y.Z., Jain, S. & Bradfield, C.A. The basic-helix-loop-helix-PAS orphan MOP3 forms transcriptionally active complexes with circadian and hypoxia factors. Proc. Natl. Acad. Sci. USA 95, 5474–5479 (1998).

    CAS  Article  Google Scholar 

  47. 47

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

    CAS  Article  Google Scholar 

  48. 48

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

    CAS  Article  Google Scholar 

  49. 49

    Daily, K., Patel, V.R., Rigor, P., Xie, X. & Baldi, P. MotifMap: integrative genome-wide maps of regulatory motif sites for model species. BMC Bioinformatics 12, 495 (2011).

    Article  Google Scholar 

  50. 50

    Hardin, P.E. Transcription regulation within the circadian clock: the E-box and beyond. J. Biol. Rhythms 19, 348–360 (2004).

    CAS  Article  Google Scholar 

  51. 51

    Hadjur, S. et al. Cohesins form chromosomal cis-interactions at the developmentally regulated IFNG locus. Nature 460, 410–413 (2009).

    CAS  Article  Google Scholar 

  52. 52

    Kosak, S.T. et al. Coordinate gene regulation during hematopoiesis is related to genomic organization. PLoS Biol. 5, e309 (2007).

    Article  Google Scholar 

  53. 53

    Cho, H. et al. Regulation of circadian behaviour and metabolism by REV-ERB-α and REV-ERB-β. Nature 485, 123–127 (2012).

    CAS  Article  Google Scholar 

  54. 54

    Eckel-Mahan, K.L. et al. Coordination of the transcriptome and metabolome by the circadian clock. Proc. Natl. Acad. Sci. USA 109, 5541–5546 (2012).

    CAS  Article  Google Scholar 

  55. 55

    Panda, S. et al. Coordinated transcription of key pathways in the mouse by the circadian clock. Cell 109, 307–320 (2002).

    CAS  Article  Google Scholar 

  56. 56

    Claudel, T., Cretenet, G., Saumet, A. & Gachon, F. Crosstalk between xenobiotics metabolism and circadian clock. FEBS Lett. 581, 3626–3633 (2007).

    CAS  Article  Google Scholar 

  57. 57

    Gachon, F., Olela, F.F., Schaad, O., Descombes, P. & Schibler, U. The circadian PAR-domain basic leucine zipper transcription factors DBP, TEF, and HLF modulate basal and inducible xenobiotic detoxification. Cell Metab. 4, 25–36 (2006).

    CAS  Article  Google Scholar 

  58. 58

    Ueda, H.R. et al. System-level identification of transcriptional circuits underlying mammalian circadian clocks. Nat. Genet. 37, 187–192 (2005).

    CAS  Article  Google Scholar 

  59. 59

    Hakim, O. et al. Spatial congregation of STAT binding directs selective nuclear architecture during T cell functional differentiation. Genome Res. 23, 462–472 (2013).

    CAS  Article  Google Scholar 

  60. 60

    Schoenfelder, S., Clay, I. & Fraser, P. The transcriptional interactome: gene expression in 3D. Curr. Opin. Genet. Dev. 20, 127–133 (2010).

    CAS  Article  Google Scholar 

  61. 61

    Hirayama, J. et al. CLOCK-mediated acetylation of BMAL1 controls circadian function. Nature 450, 1086–1090 (2007).

    CAS  Article  Google Scholar 

  62. 62

    Pando, M.P., Morse, D., Cermakian, N. & Sassone-Corsi, P. Phenotypic rescue of a peripheral clock genetic defect via SCN hierarchical dominance. Cell 110, 107–117 (2002).

    CAS  Article  Google Scholar 

  63. 63

    Grimaldi, B. et al. PER2 controls lipid metabolism by direct regulation of PPARγ. Cell Metab. 12, 509–520 (2010).

    CAS  Article  Google Scholar 

  64. 64

    Balsalobre, A. et al. Resetting of circadian time in peripheral tissues by glucocorticoid signaling. Science 289, 2344–2347 (2000).

    CAS  Article  Google Scholar 

  65. 65

    Hughes, M.E., Hogenesch, J.B. & Kornacker, K. JTK_CYCLE: an efficient nonparametric algorithm for detecting rhythmic components in genome-scale data sets. J. Biol. Rhythms 25, 372–380 (2010).

    Article  Google Scholar 

  66. 66

    Eisen, M.B., Spellman, P.T., Brown, P.O. & Botstein, D. Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. USA 95, 14863–14868 (1998).

    CAS  Article  Google Scholar 

  67. 67

    de Hoon, M.J., Imoto, S., Nolan, J. & Miyano, S. Open source clustering software. Bioinformatics 20, 1453–1454 (2004).

    CAS  Article  Google Scholar 

  68. 68

    Saeed, A.I. et al. TM4 microarray software suite. Methods Enzymol. 411, 134–193 (2006).

    CAS  Article  Google Scholar 

  69. 69

    Saeed, A.I. et al. TM4: a free, open-source system for microarray data management and analysis. Biotechniques 34, 374–378 (2003).

    CAS  Article  Google Scholar 

  70. 70

    Nogales-Cadenas, R. et al. GeneCodis: interpreting gene lists through enrichment analysis and integration of diverse biological information. Nucleic Acids Res. 37, W317–W322 (2009).

    CAS  Article  Google Scholar 

  71. 71

    Carmona-Saez, P., Chagoyen, M., Tirado, F., Carazo, J.M. & Pascual-Montano, A. GENECODIS: a web-based tool for finding significant concurrent annotations in gene lists. Genome Biol. 8, R3 (2007).

    Article  Google Scholar 

  72. 72

    Baldi, P. & Brunak, S. Bioinformatics: The Machine Learning Approach. 476 (MIT Press, 2001).

  73. 73

    Pruitt, K.D., Tatusova, T., Brown, G.R. & Maglott, D.R. NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy. Nucleic Acids Res. 40, D130–D135 (2012).

    CAS  Article  Google Scholar 

  74. 74

    Xie, X., Rigor, P. & Baldi, P. MotifMap: a human genome-wide map of candidate regulatory motif sites. Bioinformatics 25, 167–174 (2009).

    CAS  Article  Google Scholar 

  75. 75

    Matys, V. et al. TRANSFAC: transcriptional regulation, from patterns to profiles. Nucleic Acids Res. 31, 374–378 (2003).

    CAS  Article  Google Scholar 

  76. 76

    Portales-Casamar, E. et al. JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles. Nucleic Acids Res. 38, D105–D110 (2010).

    CAS  Article  Google Scholar 

  77. 77

    Krzywinski, M. et al. Circos: an information aesthetic for comparative genomics. Genome Res. 19, 1639–1645 (2009).

    CAS  Article  Google Scholar 

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We thank R.L. Schiltz and T.A. Johnson (NCI, NIH) for assisting with cell culture; R. Orozco-Solis, K. Eckel-Mahan, S. Sahar (Center for Epigenetics and Metabolism, University of California Irvine) and M. Groudine (Fred Hutchinson Cancer Research Center) for critical reading of the manuscript; S. Dilag (Center for Epigenetics and Metabolism, University of California Irvine) for technical support; X. Kong (Department of Biological Chemistry, University of California Irvine) for sharing FISH expertise and reagents; and all the members of the P.S.-C., G.L.H. and P.B. laboratories for discussions. This work was supported in part by the following grants: European Molecular Biology Organization (EMBO) long-term fellowship ALTF 411-2009 (to L.A.-A.), NIH grants R01-GM081634, AG041504 and AG033888 (to P.S.-C.) and Sirtris Pharmaceuticals grant SP-48984 (to P.S.-C.). The work of V.R.P. and P.B. is supported by the following grants: National Science Foundation grant IIS-0513376 and NIH grants LM010235-01A1 and 5T15LM007743 (to P.B.).

Author information




L.A.-A., O.H., G.L.H. and P.S.-C. conceived and designed the research. L.A.-A. and O.H. performed 4C experiments. L.A.-A. performed FISH and gene expression experimental work. L.A.-A., O.H., V.R.P. and P.B. performed bioinformatical analyses. V.R.P. performed promoter analyses using MotifMap. L.A.-A. and O.H. analyzed and interpreted the data. L.A.-A. and P.S.-C. wrote the manuscript.

Corresponding authors

Correspondence to Pierre Baldi or Paolo Sassone-Corsi.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–6 (PDF 6704 kb)

Supplementary Table 1

4C genomic regions that interact in trans with Dbp (XLSX 35 kb)

Supplementary Table 2

Gene content of Dbp contacts detected in wild type MEFs (XLSX 240 kb)

Supplementary Table 3

Dbp circadian interactome (XLSX 30 kb)

Supplementary Table 4

Motif Map analyses on 4C contact regions (XLSX 4286 kb)

Supplementary Table 5

p scores at the region analyzed by FISH (XLSX 20 kb)

Supplementary Table 6

Circadian gene expression in wild type MEFs (XLSX 6515 kb)

Supplementary Table 7

Ontological analyses (XLSX 32 kb)

Supplementary Table 8

Lists of circadian genes (XLSX 120 kb)

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Aguilar-Arnal, L., Hakim, O., Patel, V. et al. Cycles in spatial and temporal chromosomal organization driven by the circadian clock. Nat Struct Mol Biol 20, 1206–1213 (2013).

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