Brain Structure and Function

, Volume 218, Issue 2, pp 551–562 | Cite as

Circadian clock components in the rat neocortex: daily dynamics, localization and regulation

  • Martin F. Rath
  • Kristian Rohde
  • Jan Fahrenkrug
  • Morten Møller
Original Article


The circadian master clock of the mammalian brain resides in the suprachiasmatic nucleus (SCN) of the hypothalamus. At the molecular level, the clock of the SCN is driven by a transcriptional/posttranslational autoregulatory network with clock gene products as core elements. Recent investigations have shown the presence of peripheral clocks in extra-hypothalamic areas of the central nervous system. However, knowledge on the clock gene network in the cerebral cortex is limited. We here show that the mammalian clock genes Per1, Per2, Per3, Cry1, Cry2, Bmal1, Clock, Nr1d1 and Dbp are expressed in the rat neocortex. Among these, Per1, Per2, Per3, Cry1, Bmal1, Nr1d1 and Dbp were found to exhibit daily rhythms. The amplitude of circadian oscillation in neocortical clock gene expression was damped and the peak delayed as compared with the SCN. Lesions of the SCN revealed that rhythmic clock gene expression in the neocortex is dependent on the SCN. In situ hybridization and immunohistochemistry showed that products of the canonical clock gene Per2 are located in perikarya throughout all areas of the neocortex. These findings show that local circadian oscillators driven by the SCN reside within neurons of the neocortex.


Cerebral cortex Circadian rhythm Clock gene Peripheral oscillator Suprachiasmatic nucleus 



Dark–dark lighting regime (constant darkness)


Light–dark lighting regime


Quantitative real-time reverse-transcription PCR


Suprachiasmatic nucleus


Zeitgeber time



This work was supported by the Danish Medical Research Council (grants number 271-09-0206 and 271-07-0412) and the Lundbeck Foundation (grant number R34-A3364). We wish to thank Ms. Tine Thorup Mellergaard for expert technical assistance.

Supplementary material

429_2012_415_MOESM1_ESM.pdf (444 kb)
Supplementary material 1 (PDF 444 kb)


  1. Abe H, Honma S, Namihira M, Tanahashi Y, Ikeda M, Honma K-i (1998) Circadian rhythm and light responsiveness of BMAL1 expression, a partner of mammalian clock gene Clock, in the suprachiasmatic nucleus of rats. Neurosci Lett 258:93–96PubMedCrossRefGoogle Scholar
  2. Abe H, Honma S, Namihira M, Masubuchi S, Ikeda M, Ebihara S, Honma K-i (2001) Clock gene expressions in the suprachiasmatic nucleus and other areas of the brain during rhythm splitting in CS mice. Mol Brain Res 87:92–99PubMedCrossRefGoogle Scholar
  3. Abe M, Herzog ED, Yamazaki S, Straume M, Tei H, Sakaki Y, Menaker M, Block GD (2002) Circadian rhythms in isolated brain regions. J Neurosci 22:350–356PubMedGoogle Scholar
  4. Abe H, Honma S, Ohtsu H, Honma K-i (2004) Circadian rhythms in behavior and clock gene expressions in the brain of mice lacking histidine decarboxylase. Mol Brain Res 124:178–187PubMedCrossRefGoogle Scholar
  5. Abraham U, Prior JL, Granados-Fuentes D, Piwnica-Worms DR, Herzog ED (2005) Independent circadian oscillations of Period1 in specific brain areas in vivo and in vitro. J Neurosci 25:8620–8626PubMedCrossRefGoogle Scholar
  6. Albrecht U, Sun ZS, Eichele G, Lee CC (1997) A differential response of two putative mammalian circadian regulators, mper1 and mper2, to light. Cell 91:1055–1064PubMedCrossRefGoogle Scholar
  7. Angeles-Castellanos M, Mendoza J, Escobar C (2007) Restricted feeding schedules phase shift daily rhythms of c-Fos and protein Per1 immunoreactivity in corticolimbic regions in rats. Neuroscience 144:344–355PubMedCrossRefGoogle Scholar
  8. Antoch MP, Song E-J, Chang A-M, Vitaterna MH, Zhao Y, Wilsbacher LD, Sangoram AM, King DP, Pinto LH, Takahashi JS (1997) Functional identification of the mouse circadian clock gene by transgenic BAC rescue. Cell 89:655–667PubMedCrossRefGoogle Scholar
  9. Asai M, Yoshinobu Y, Kaneko S, Mori A, Nikaido T, Moriya T, Akiyama M, Shibata S (2001) Circadian profile of Per gene mRNA expression in the suprachiasmatic nucleus, paraventricular nucleus, and pineal body of aged rats. J Neurosci Res 66:1133–1139PubMedCrossRefGoogle Scholar
  10. Aton SJ, Herzog ED (2005) Come together, right…now: synchronization of rhythms in a mammalian circadian clock. Neuron 48:531–534PubMedCrossRefGoogle Scholar
  11. Bass J, Takahashi JS (2010) Circadian integration of metabolism and energetics. Science 330:1349–1354PubMedCrossRefGoogle Scholar
  12. Buhr ED, Yoo S-H, Takahashi JS (2010) Temperature as a universal resetting cue for mammalian circadian oscillators. Science 330:379–385PubMedCrossRefGoogle Scholar
  13. Bunger MK, Wilsbacher LD, Moran SM, Clendenin C, Radcliffe LA, Hogenesch JB, Simon MC, Takahashi JS, Bradfield CA (2000) Mop3 is an essential component of the master circadian pacemaker in mammals. Cell 103:1009–1017PubMedCrossRefGoogle Scholar
  14. Bunney JN, Potkin SG (2008) Circadian abnormalities, molecular clock genes and chronobiological treatments in depression. Br Med Bull 86:23–32PubMedCrossRefGoogle Scholar
  15. Coogan AN, Papachatzaki MM, Clemens C, Baird A, Donev RM, Joosten J, Zachariou V, Thome J (2011) Haloperidol alters circadian clock gene product expression in the mouse brain. World J Biol Psychiatry 12:638–644PubMedCrossRefGoogle Scholar
  16. DeFelipe J (1997) Types of neurons, synaptic connections and chemical characteristics of cells immunoreactive for calbindin-D28K, parvalbumin and calretinin in the neocortex. J Chem Neuroanat 14:1–19PubMedCrossRefGoogle Scholar
  17. Druga R (2009) Neocortical inhibitory system. Folia Biol (Praha) 55:201–217Google Scholar
  18. Fahrenkrug J, Georg B, Hannibal J, Hindersson P, Gras S (2006) Diurnal rhythmicity of the clock genes Per1 and Per2 in the rat ovary. Endocrinology 147:3769–3776PubMedCrossRefGoogle Scholar
  19. Gekakis N, Staknis D, Nguyen HB, Davis FC, Wilsbacher LD, King DP, Takahashi JS, Weitz CJ (1998) Role of the CLOCK protein in the mammalian circadian mechanism. Science 280:1564–1569PubMedCrossRefGoogle Scholar
  20. Gooley JJ, Lu J, Chou TC, Scammell TE, Saper CB (2001) Melanopsin in cells of origin of the retinohypothalamic tract. Nat Neurosci 4:1165PubMedCrossRefGoogle Scholar
  21. Granados-Fuentes D, Prolo LM, Abraham U, Herzog ED (2004) The suprachiasmatic nucleus entrains, but does not sustain, circadian rhythmicity in the olfactory bulb. J Neurosci 24:615–619PubMedCrossRefGoogle Scholar
  22. Green CB, Takahashi JS, Bass J (2008) The meter of metabolism. Cell 134:728–742PubMedCrossRefGoogle Scholar
  23. Guilding C, Piggins HD (2007) Challenging the omnipotence of the suprachiasmatic timekeeper: are circadian oscillators present throughout the mammalian brain? Eur J Neurosci 25:3195–3216PubMedCrossRefGoogle Scholar
  24. Hannibal J, Hindersson P, Knudsen SM, Georg B, Fahrenkrug J (2002) The photopigment melanopsin is exclusively present in pituitary adenylate cyclase-activating polypeptide-containing retinal ganglion cells of the retinohypothalamic tract. J Neurosci 22:RC191Google Scholar
  25. Hastings MH, Maywood ES, O’Neill JS (2008) Cellular circadian pacemaking and the role of cytosolic rhythms. Curr Biol 18:R805–R815PubMedCrossRefGoogle Scholar
  26. Hattar S, Lucas RJ, Mrosovsky N, Thompson S, Douglas RH, Hankins MW, Lem J, Biel M, Hofmann F, Foster RG, Yau KW (2003) Melanopsin and rod-cone photoreceptive systems account for all major accessory visual functions in mice. Nature 424:76–81PubMedCrossRefGoogle Scholar
  27. Honma S, Ikeda M, Abe H, Tanahashi Y, Namihira M, Honma K, Nomura M (1998) Circadian oscillation of BMAL1, a partner of a mammalian clock gene Clock, in rat suprachiasmatic nucleus. Biochem Biophys Res Commun 250:83–87PubMedCrossRefGoogle Scholar
  28. Hood S, Cassidy P, Cossette M-P, Weigl Y, Verwey M, Robinson B, Stewart J, Amir S (2010) Endogenous dopamine regulates the rhythm of expression of the clock protein PER2 in the rat dorsal striatum via daily activation of D2 dopamine receptors. J Neurosci 30:14046–14058PubMedCrossRefGoogle Scholar
  29. Imbesi M, Yildiz S, Dirim Arslan A, Sharma R, Manev H, Uz T (2009) Dopamine receptor-mediated regulation of neuronal “clock” gene expression. Neuroscience 158:537–544PubMedCrossRefGoogle Scholar
  30. Jilg A, Lesny S, Peruzki N, Schwegler H, Selbach O, Dehghani F, Stehle JH (2010) Temporal dynamics of mouse hippocampal clock gene expression support memory processing. Hippocampus 20:377–388PubMedGoogle Scholar
  31. Johnston-Wilson NL, Sims CD, Hofmann JP, Anderson L, Shore AD, Torrey EF, Yolken RH (2000) Disease-specific alterations in frontal cortex brain proteins in schizophrenia, bipolar disorder, and major depressive disorder. The Stanley Neuropathology Consortium. Mol Psychiatry 5:142–149PubMedCrossRefGoogle Scholar
  32. Kawaguchi Y, Kubota Y (1997) GABAergic cell subtypes and their synaptic connections in rat frontal cortex. Cereb Cortex 7:476–486PubMedCrossRefGoogle Scholar
  33. King DP, Zhao Y, Sangoram AM, Wilsbacher LD, Tanaka M, Antoch MP, Steeves TDL, Vitaterna MH, Kornhauser JM, Lowrey PL, Turek FW, Takahashi JS (1997) Positional cloning of the mouse circadian clock gene. Cell 89:641–653PubMedCrossRefGoogle Scholar
  34. Klein DC, Moore RY (1979) Pineal N-acetyltransferase and hydroxyindole-O-methyltransferase: control by the retinohypothalamic tract and the suprachiasmatic nucleus. Brain Res 174:245–262PubMedCrossRefGoogle Scholar
  35. Klein DC, Bailey MJ, Carter DA, Kim JS, Shi Q, Ho AK, Chik CL, Gaildrat P, Morin F, Ganguly S, Rath MF, Møller M, Sugden D, Rangel ZG, Munson PJ, Weller JL, Coon SL (2010) Pineal function: impact of microarray analysis. Mol Cell Endocrinol 314:170–183PubMedCrossRefGoogle Scholar
  36. Lopez-Molina L, Conquet F, Dubois-Dauphin M, Schibler U (1997) The DBP gene is expressed according to a circadian rhythm in the suprachiasmatic nucleus and influences circadian behavior. EMBO J 16:6762–6771PubMedCrossRefGoogle Scholar
  37. Masubuchi S, Honma S, Abe H, Ishizaki K, Namihira M, Ikeda M, Honma K-i (2000) Clock genes outside the suprachiasmatic nucleus involved in manifestation of locomotor activity rhythm in rats. Eur J Neurosci 12:4206–4214PubMedGoogle Scholar
  38. Matsui D, Takekida S, Okamura H (2005) Molecular oscillation of Per1 and Per2 genes in the rodent brain: an in situ hybridization and molecular biological study. Kobe J Med Sci 51:85–93PubMedGoogle Scholar
  39. Maywood ES, Chesham JE, O’Brien JA, Hastings MH (2011) A diversity of paracrine signals sustains molecular circadian cycling in suprachiasmatic nucleus circuits. Proc Natl Acad Sci USA 108:14306–14311PubMedCrossRefGoogle Scholar
  40. Miyamoto Y, Sancar A (1998) Vitamin B2-based blue-light photoreceptors in the retinohypothalamic tract as the photoactive pigments for setting the circadian clock in mammals. Proc Natl Acad Sci USA 95:6097–6102PubMedCrossRefGoogle Scholar
  41. Mohawk JA, Takahashi JS (2011) Cell autonomy and synchrony of suprachiasmatic nucleus circadian oscillators. Trends Neurosci 34:349–358CrossRefGoogle Scholar
  42. Møller M, Baeres F (2002) The anatomy and innervation of the mammalian pineal gland. Cell Tissue Res 309:139–150PubMedCrossRefGoogle Scholar
  43. Moore RY, Eichler VB (1972) Loss of a circadian adrenal corticosterone rhythm following suprachiasmatic lesions in the rat. Brain Res 42:201–206PubMedCrossRefGoogle Scholar
  44. Moore RY, Lenn NJ (1972) A retinohypothalamic projection in the rat. J Comp Neurol 146:1–14PubMedCrossRefGoogle Scholar
  45. Namihira M, Honma S, Abe H, Tanahashi Y, Ikeda M, Honma K-I (1999) Daily variation and light responsiveness of mammalian clock gene, clock and BMAL1, transcripts in the pineal body and different areas of brain in rats. Neurosci Lett 267:69–72PubMedCrossRefGoogle Scholar
  46. Okamura H, Miyake S, Sumi Y, Yamaguchi S, Yasui A, Muijtjens M, Hoeijmakers JHJ, van der Horst GTJ (1999) Photic Induction of mPer1 and mPer2 in Cry-deficient mice lacking a biological clock. Science 286:2531–2534PubMedCrossRefGoogle Scholar
  47. Onishi H, Yamaguchi S, Yagita K, Ishida Y, Dong X, Kimura H, Jing Z, Ohara H, Okamura H (2002) Rev-erbα gene expression in the mouse brain with special emphasis on its circadian profiles in the suprachiasmatic nucleus. J Neurosci Res 68:551–557PubMedCrossRefGoogle Scholar
  48. Preitner N, Damiola F, Luis Lopez M, Zakany J, Duboule D, Albrecht U, Schibler U (2002) The orphan nuclear receptor REV-ERBα controls circadian transcription within the positive limb of the mammalian circadian oscillator. Cell 110:251–260PubMedCrossRefGoogle Scholar
  49. Rath MF, Morin F, Shi Q, Klein DC, Møller M (2007) Ontogenetic expression of the Otx2 and Crx homeobox genes in the retina of the rat. Exp Eye Res 85:65–73PubMedCrossRefGoogle Scholar
  50. Rath MF, Bailey MJ, Kim JS, Ho AK, Gaildrat P, Coon SL, Møller M, Klein DC (2009a) Developmental and diurnal dynamics of Pax4 expression in the mammalian pineal gland: nocturnal down-regulation is mediated by adrenergic-cyclic adenosine 3′,5′-monophosphate signaling. Endocrinology 150:803–811PubMedCrossRefGoogle Scholar
  51. Rath MF, Bailey MJ, Kim JS, Coon SL, Klein DC, Møller M (2009b) Developmental and daily expression of the Pax4 and Pax6 homeobox genes in the rat retina: localization of Pax4 in photoreceptor cells. J Neurochem 108:285–294PubMedCrossRefGoogle Scholar
  52. Reppert SM, Weaver DR (2002) Coordination of circadian timing in mammals. Nature 418:935–941PubMedCrossRefGoogle Scholar
  53. Rovsing L, Rath MF, Lund-Andersen C, Klein DC, Møller M (2010) A neuroanatomical and physiological study of the non-image forming visual system of the cone-rod homeobox gene (Crx) knock out mouse. Brain Res 1343:54–65PubMedCrossRefGoogle Scholar
  54. Saper CB, Lu J, Chou TC, Gooley J (2005) The hypothalamic integrator for circadian rhythms. Trends Neurosci 28:152–157PubMedCrossRefGoogle Scholar
  55. Segall L, Amir S (2010) Glucocorticoid regulation of clock gene expression in the mammalian limbic forebrain. J Mol Neurosci 42:168–175PubMedCrossRefGoogle Scholar
  56. Shearman LP, Zylka MJ, Weaver DR, Kolakowski LF Jr, Reppert SM (1997) Two period homologs: circadian expression and photic regulation in the suprachiasmatic nuclei. Neuron 19:1261–1269PubMedCrossRefGoogle Scholar
  57. Shearman LP, Zylka MJ, Reppert SM, Weaver DR (1999) Expression of basic helix-loop-helix/PAS genes in the mouse suprachiasmatic nucleus. Neuroscience 89:387–397PubMedCrossRefGoogle Scholar
  58. Shearman LP, Sriram S, Weaver DR, Maywood ES, Chaves I, Zheng B, Kume K, Lee CC, van der Horst GT, Hastings MH, Reppert SM (2000) Interacting molecular loops in the mammalian circadian clock. Science 288:1013–1019PubMedCrossRefGoogle Scholar
  59. Shieh KR (2003) Distribution of the rhythm-related genes rPERIOD1, rPERIOD2, and rCLOCK, in the rat brain. Neuroscience 118:831–843PubMedCrossRefGoogle Scholar
  60. Simonneaux V, Poirel VJ, Garidou ML, Nguyen D, Diaz-Rodriguez E, Pévet P (2004) Daily rhythm and regulation of clock gene expression in the rat pineal gland. Mol Brain Res 120:164–172PubMedCrossRefGoogle Scholar
  61. Son GH, Chung S, Kim K (2011) The adrenal peripheral clock: glucocorticoid and the circadian timing system. Front Neuroendocrinol 32:451–465PubMedCrossRefGoogle Scholar
  62. Stephan FK, Zucker I (1972) Circadian rhythms in drinking behavior and locomotor activity of rats are eliminated by hypothalamic lesions. Proc Natl Acad Sci USA 69:1583–1586PubMedCrossRefGoogle Scholar
  63. Sun ZS, Albrecht U, Zhuchenko O, Bailey J, Eichele G, Lee CC (1997) RIGUI, a putative mammalian ortholog of the Drosophila period gene. Cell 90:1003–1011PubMedCrossRefGoogle Scholar
  64. Takekida S, Yan L, Maywood ES, Hastings MH, Okamura H (2000) Differential adrenergic regulation of the circadian expression of the clock genes Period1 and Period2 in the rat pineal gland. Eur J Neurosci 12:4557–4561PubMedCrossRefGoogle Scholar
  65. Takumi T, Taguchi K, Miyake S, Sakakida Y, Takashima N, Matsubara C, Maebayashi Y, Okumura K, Takekida S, Yamamoto S, Yagita K, Yan L, Young M, Okamura H (1998) A light-independent oscillatory gene mPer3 in mouse SCN and OVLT. EMBO J 17:4753–4759PubMedCrossRefGoogle Scholar
  66. Terazono H, Mutoh T, Yamaguchi S, Kobayashi M, Akiyama M, Udo R, Ohdo S, Okamura H, Shibata S (2003) Adrenergic regulation of clock gene expression in mouse liver. Proc Natl Acad Sci USA 100:6795–6800PubMedCrossRefGoogle Scholar
  67. Thresher RJ, Vitaterna MH, Miyamoto Y, Kazantsev A, Hsu DS, Petit C, Selby CP, Dawut L, Smithies O, Takahashi JS, Sancar A (1998) Role of mouse cryptochrome blue-light photoreceptor in circadian photoresponses. Science 282:1490–1494PubMedCrossRefGoogle Scholar
  68. Tonsfeldt KJ, Chappell PE (2012) Clocks on top: the role of the circadian clock in the hypothalamic and pituitary regulation of endocrine physiology. Mol Cell Endocrinol 349:3–12PubMedCrossRefGoogle Scholar
  69. Tosini G, Menaker M (1996) Circadian rhythms in cultured mammalian retina. Science 272:419–421PubMedCrossRefGoogle Scholar
  70. Tosini G, Kasamatsu M, Sakamoto K (2007) Clock gene expression in the rat retina: effects of lighting conditions and photoreceptor degeneration. Brain Res 1159:134–140PubMedCrossRefGoogle Scholar
  71. Verwey M, Amir S (2009) Food-entrainable circadian oscillators in the brain. Eur J Neurosci 30:1650–1657PubMedCrossRefGoogle Scholar
  72. Vitaterna M, King D, Chang A, Kornhauser J, Lowrey P, McDonald J, Dove W, Pinto L, Turek F, Takahashi J (1994) Mutagenesis and mapping of a mouse gene, clock, essential for circadian behavior. Science 264:719–725PubMedCrossRefGoogle Scholar
  73. Vrang N, Larsen PJ, Møller M, Mikkelsen JD (1995) Topographical organization of the rat suprachiasmatic-paraventriocular projection. J Comp Neurol 353:585–603PubMedCrossRefGoogle Scholar
  74. Wakamatsu H, Yoshinobu Y, Aida R, Moriya T, Akiyama M, Shibata S (2001) Restricted-feeding-induced anticipatory activity rhythm is associated with a phase-shift of the expression of mPer1 and mPer2 mRNA in the cerebral cortex and hippocampus but not in the suprachiasmatic nucleus of mice. Eur J Neurosci 13:1190–1196PubMedCrossRefGoogle Scholar
  75. Welsh DK, Logothetis DE, Meister M, Reppert SM (1995) Individual neurons dissociated from rat suprachiasmatic nucleus express independently phased circadian firing rhythms. Neuron 14:697–706PubMedCrossRefGoogle Scholar
  76. Wirz-Justice A (1995) Biological rhythms in mood disorders. In: Bloom F (ed) Psychopharmacology: the fourth generation of progress. Raven Press, New York, pp 999–1017Google Scholar
  77. Wisor JP, Pasumarthi RK, Gerashchenko D, Thompson CL, Pathak S, Sancar A, Franken P, Lein ES, Kilduff TS (2008) Sleep deprivation effects on circadian clock gene expression in the cerebral cortex parallel electroencephalographic differences among mouse strains. J Neurosci 28:7193–7201PubMedCrossRefGoogle Scholar
  78. Wulff K, Gatti S, Wettstein JG, Foster RG (2010) Sleep and circadian rhythm disruption in psychiatric and neurodegenerative disease. Nat Rev Neurosci 11:589–599PubMedCrossRefGoogle Scholar
  79. Yamamoto T, Nakahata Y, Soma H, Akashi M, Mamine T, Takumi T (2004) Transcriptional oscillation of canonical clock genes in mouse peripheral tissues. BMC Mol Biol 5:18PubMedCrossRefGoogle Scholar
  80. Yang S, Wang K, Valladares O, Hannenhalli S, Bucan M (2007) Genome-wide expression profiling and bioinformatics analysis of diurnally regulated genes in the mouse prefrontal cortex. Genome Biol 8:R247PubMedCrossRefGoogle Scholar
  81. Zhang EE, Kay SA (2010) Clocks not winding down: unravelling circadian networks. Nat Rev Mol Cell Biol 11:764–776PubMedCrossRefGoogle Scholar
  82. Zheng B, Larkin DW, Albrecht U, Sun ZS, Sage M, Eichele G, Lee CC, Bradley A (1999) The mPer2 gene encodes a functional component of the mammalian circadian clock. Nature 400:169–173PubMedCrossRefGoogle Scholar
  83. Zheng B, Albrecht U, Kaasik K, Sage M, Lu W, Vaishnav S, Li Q, Sun ZS, Eichele G, Bradley A, Lee CC (2001) Nonredundant roles of the mPer1 and mPer2 genes in the mammalian circadian clock. Cell 105:683–694PubMedCrossRefGoogle Scholar

Copyright information

© Springer-Verlag 2012

Authors and Affiliations

  • Martin F. Rath
    • 1
  • Kristian Rohde
    • 1
  • Jan Fahrenkrug
    • 2
  • Morten Møller
    • 1
  1. 1.Department of Neuroscience and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Panum Institute 24.2CopenhagenDenmark
  2. 2.Department of Clinical Biochemistry, Faculty of Health and Medical Sciences, University of Copenhagen, Bispebjerg HospitalCopenhagenDenmark

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