Skip to main content

2015 | OriginalPaper | Buchkapitel

Model-Based Investigation of the Effect of the Cell Cycle on the Circadian Clock Through Transcription Inhibition During Mitosis

verfasst von : Pauline Traynard, François Fages, Sylvain Soliman

Erschienen in: Computational Methods in Systems Biology

Verlag: Springer International Publishing

Aktivieren Sie unsere intelligente Suche, um passende Fachinhalte oder Patente zu finden.

search-config
loading …

Abstract

Experimental observations have put in evidence autonomous self-sustained circadian oscillators in most mammalian cells, and proved the existence of molecular links between the circadian clock and the cell cycle. Several models have been elaborated to assess conditions of control of the cell cycle by the circadian clock, in particular through the regulation by clock genes of Wee1, an inhibitor of the mitosis promoting factor, responsible for a circadian gating of mitosis and cell division period doubling phenomena. However, recent studies in individual NIH3T3 fibroblasts have shown an unexpected acceleration of the circadian clock together with the cell cycle when the milieu is enriched in FBS, the absence of such acceleration in confluent cells, and the absence of any period doubling phenomena. In this paper, we try to explain these observations by a possible entrainment of the circadian clock by the cell cycle through the inhibition of transcription during mitosis. We develop a differential model of that reverse coupling of the cell cycle and the circadian clock and investigate the conditions in which both cycles are mutually entrained. We use the mammalian circadian clock model of Relogio et al. and a simple model of the cell cycle by Qu et al. which focuses on the mitosis phase. We show that our coupled model is able to reproduce the main observations reported by Feillet et al. in individual fibroblast experiments and use it for making some predictions.

Sie haben noch keine Lizenz? Dann Informieren Sie sich jetzt über unsere Produkte:

Springer Professional "Wirtschaft+Technik"

Online-Abonnement

Mit Springer Professional "Wirtschaft+Technik" erhalten Sie Zugriff auf:

  • über 102.000 Bücher
  • über 537 Zeitschriften

aus folgenden Fachgebieten:

  • Automobil + Motoren
  • Bauwesen + Immobilien
  • Business IT + Informatik
  • Elektrotechnik + Elektronik
  • Energie + Nachhaltigkeit
  • Finance + Banking
  • Management + Führung
  • Marketing + Vertrieb
  • Maschinenbau + Werkstoffe
  • Versicherung + Risiko

Jetzt Wissensvorsprung sichern!

Springer Professional "Technik"

Online-Abonnement

Mit Springer Professional "Technik" erhalten Sie Zugriff auf:

  • über 67.000 Bücher
  • über 390 Zeitschriften

aus folgenden Fachgebieten:

  • Automobil + Motoren
  • Bauwesen + Immobilien
  • Business IT + Informatik
  • Elektrotechnik + Elektronik
  • Energie + Nachhaltigkeit
  • Maschinenbau + Werkstoffe




 

Jetzt Wissensvorsprung sichern!

Springer Professional "Wirtschaft"

Online-Abonnement

Mit Springer Professional "Wirtschaft" erhalten Sie Zugriff auf:

  • über 67.000 Bücher
  • über 340 Zeitschriften

aus folgenden Fachgebieten:

  • Bauwesen + Immobilien
  • Business IT + Informatik
  • Finance + Banking
  • Management + Führung
  • Marketing + Vertrieb
  • Versicherung + Risiko




Jetzt Wissensvorsprung sichern!

Fußnoten
1
The models and the specification used in this paper are available on http://​lifeware.​inria.​fr/​wiki/​software/​cmsb15.
 
Literatur
1.
Zurück zum Zitat Ballesta, A., Dulong, S., Abbara, C., Cohen, B., Okyar, A., Clairambault, J., Levi, F.: A combined experimental and mathematical approach for molecular-based optimization of irinotecan circadian delivery. PLOS Comput. Biol. 7(9), e1002143 (2011)MathSciNetCrossRef Ballesta, A., Dulong, S., Abbara, C., Cohen, B., Okyar, A., Clairambault, J., Levi, F.: A combined experimental and mathematical approach for molecular-based optimization of irinotecan circadian delivery. PLOS Comput. Biol. 7(9), e1002143 (2011)MathSciNetCrossRef
2.
Zurück zum Zitat Barnes, J.W., Tischkau, S.A., Barnes, J.A., Mitchell, J.W., Burgoon, P.W., Hickok, J.R., Gillette, M.U.: Requirement of mammalian timeless for circadian rhythmicity. Science 302(5644), 439–442 (2003)CrossRef Barnes, J.W., Tischkau, S.A., Barnes, J.A., Mitchell, J.W., Burgoon, P.W., Hickok, J.R., Gillette, M.U.: Requirement of mammalian timeless for circadian rhythmicity. Science 302(5644), 439–442 (2003)CrossRef
3.
Zurück zum Zitat Bieler, J., Cannavo, R., Gustafson, K., Gobet, C., Gatfield, D., Naef, F.: Robust synchronization of coupled circadian and cell cycle oscillators in single mammalian cells. Mol. Syst. Biol. 10(7), 739 (2014)CrossRef Bieler, J., Cannavo, R., Gustafson, K., Gobet, C., Gatfield, D., Naef, F.: Robust synchronization of coupled circadian and cell cycle oscillators in single mammalian cells. Mol. Syst. Biol. 10(7), 739 (2014)CrossRef
4.
Zurück zum Zitat Calzone, L., Chabrier-Rivier, N., Fages, F., Soliman, S.: Machine learning biochemical networks from temporal logic properties. In: Priami, C., Plotkin, G. (eds.) Transactions on Computational Systems Biology VI. LNCS (LNBI), vol. 4220, pp. 68–94. Springer, Heidelberg (2006) CrossRef Calzone, L., Chabrier-Rivier, N., Fages, F., Soliman, S.: Machine learning biochemical networks from temporal logic properties. In: Priami, C., Plotkin, G. (eds.) Transactions on Computational Systems Biology VI. LNCS (LNBI), vol. 4220, pp. 68–94. Springer, Heidelberg (2006) CrossRef
5.
Zurück zum Zitat Calzone, L., Fages, F., Soliman, S.: BIOCHAM: An environment for modeling biological systems and formalizing experimental knowledge. Bioinformatics 22(14), 1805–1807 (2006)CrossRef Calzone, L., Fages, F., Soliman, S.: BIOCHAM: An environment for modeling biological systems and formalizing experimental knowledge. Bioinformatics 22(14), 1805–1807 (2006)CrossRef
6.
Zurück zum Zitat Calzone, L., Soliman, S.: Coupling the cell cycle and the circadian cycle. Research Report 5835, INRIA, February 2006 Calzone, L., Soliman, S.: Coupling the cell cycle and the circadian cycle. Research Report 5835, INRIA, February 2006
7.
Zurück zum Zitat De Maria, E., Fages, F., Rizk, A., Soliman, S.: Design, optimization, and predictions of a coupled model of the cell cycle, circadian clock, dna repair system, irinotecan metabolism and exposure control under temporal logic constraints. Theor. Comput. Sci. 412(21), 2108–2127 (2011)CrossRefMATH De Maria, E., Fages, F., Rizk, A., Soliman, S.: Design, optimization, and predictions of a coupled model of the cell cycle, circadian clock, dna repair system, irinotecan metabolism and exposure control under temporal logic constraints. Theor. Comput. Sci. 412(21), 2108–2127 (2011)CrossRefMATH
8.
Zurück zum Zitat Emi, N., Camille, S., Christoph, B., Thierry, L., Felix, N., Schibler, U.: Circadian gene expression in individual fibroblasts: cell-autonomous and self-sustained oscillators pass time to daughter cells. Cell 119, 693–705 (2004)CrossRef Emi, N., Camille, S., Christoph, B., Thierry, L., Felix, N., Schibler, U.: Circadian gene expression in individual fibroblasts: cell-autonomous and self-sustained oscillators pass time to daughter cells. Cell 119, 693–705 (2004)CrossRef
9.
Zurück zum Zitat Fages, F., Rizk, A.: On temporal logic constraint solving for the analysis of numerical data time series. Theor. Comput. Sci. 408(1), 55–65 (2008)MathSciNetCrossRefMATH Fages, F., Rizk, A.: On temporal logic constraint solving for the analysis of numerical data time series. Theor. Comput. Sci. 408(1), 55–65 (2008)MathSciNetCrossRefMATH
10.
Zurück zum Zitat Fages, F., Traynard, P.: Temporal logic modeling of dynamical behaviors: first-order patterns and solvers. In: del Cerro, L.F., Inoue, K. (eds.) Logical Modeling of Biological Systems, Chapter 8, pp. 291–323. Wiley, New York (2014) Fages, F., Traynard, P.: Temporal logic modeling of dynamical behaviors: first-order patterns and solvers. In: del Cerro, L.F., Inoue, K. (eds.) Logical Modeling of Biological Systems, Chapter 8, pp. 291–323. Wiley, New York (2014)
11.
Zurück zum Zitat Feillet, C., Krusche, P., Tamanini, F., Janssens, R.C., Downey, M.J., Martin, P., Teboul, M., Saito, S., Lévi, F.A., Bretschneider, T., van der Horst, G.T.J., Delaunay, F., Rand, D.A.: Phase locking and multiple oscillating attractors for the coupled mammalian clock and cell cycle. Proc. Nat. Acad. Sci. U.S.A 111(27), 9833–9928 (2014)CrossRef Feillet, C., Krusche, P., Tamanini, F., Janssens, R.C., Downey, M.J., Martin, P., Teboul, M., Saito, S., Lévi, F.A., Bretschneider, T., van der Horst, G.T.J., Delaunay, F., Rand, D.A.: Phase locking and multiple oscillating attractors for the coupled mammalian clock and cell cycle. Proc. Nat. Acad. Sci. U.S.A 111(27), 9833–9928 (2014)CrossRef
12.
Zurück zum Zitat Gérard, C., Goldbeter, A.: Entrainment of the mammalian cell cycle by the circadian clock: modeling two coupled cellular rhythms. PLoS Comput. Biol. 8(21), e1002516 (2012)CrossRef Gérard, C., Goldbeter, A.: Entrainment of the mammalian cell cycle by the circadian clock: modeling two coupled cellular rhythms. PLoS Comput. Biol. 8(21), e1002516 (2012)CrossRef
13.
Zurück zum Zitat Glass, L.: Synchronization and rhythmic processes in physiology. Nature 410(6825), 277–284 (2001)CrossRef Glass, L.: Synchronization and rhythmic processes in physiology. Nature 410(6825), 277–284 (2001)CrossRef
14.
Zurück zum Zitat Gréchez-Cassiau, A., Rayet, B., Guillaumond, F., Teboul, M., Delaunay, F.: The circadian clock component bmal1 is a critical regulator of p21WAF1/CIP1 expression and hepatocyte proliferation. J. Biol. Chem. 283, 4535–4542 (2008)CrossRef Gréchez-Cassiau, A., Rayet, B., Guillaumond, F., Teboul, M., Delaunay, F.: The circadian clock component bmal1 is a critical regulator of p21WAF1/CIP1 expression and hepatocyte proliferation. J. Biol. Chem. 283, 4535–4542 (2008)CrossRef
15.
Zurück zum Zitat Kang, B., Li, Y.-Y., Chang, X., Liu, L., Li, Y.-X.: Modeling the effects of cell cycle m-phase transcriptional inhibition on circadian oscillation. PLoS Comput. Biol. 4(3), e1000019 (2008)MathSciNetCrossRef Kang, B., Li, Y.-Y., Chang, X., Liu, L., Li, Y.-X.: Modeling the effects of cell cycle m-phase transcriptional inhibition on circadian oscillation. PLoS Comput. Biol. 4(3), e1000019 (2008)MathSciNetCrossRef
16.
Zurück zum Zitat Matsuo, T., Yamaguchi, S., Mitsui, S., Emi, A., Shimoda, F., Okamura, H.: Control mechanism of the circadian clock for timing of cell division in vivo. Science 302(5643), 255–259 (2003)CrossRef Matsuo, T., Yamaguchi, S., Mitsui, S., Emi, A., Shimoda, F., Okamura, H.: Control mechanism of the circadian clock for timing of cell division in vivo. Science 302(5643), 255–259 (2003)CrossRef
17.
Zurück zum Zitat Perez-Roger, I.: Myc activation of cyclin e/cdk2 kinase involves induction of cyclin e gene transcription and inhibition of p27(kip1) binding to newly formed complexes. Oncogene 14(20), 2373–81 (1997)CrossRef Perez-Roger, I.: Myc activation of cyclin e/cdk2 kinase involves induction of cyclin e gene transcription and inhibition of p27(kip1) binding to newly formed complexes. Oncogene 14(20), 2373–81 (1997)CrossRef
18.
Zurück zum Zitat Qu, Z., MacLellan, W.R., Weiss, J.N.: Dynamics of the cell cycle: checkpoints, sizers, and timers. Biophys. J. 85(6), 3600–3611 (2003)CrossRef Qu, Z., MacLellan, W.R., Weiss, J.N.: Dynamics of the cell cycle: checkpoints, sizers, and timers. Biophys. J. 85(6), 3600–3611 (2003)CrossRef
19.
Zurück zum Zitat Relógio, A., Westermark, P.O., Wallach, T., Schellenberg, K., Kramer, A., Herzel, H.: Tuning the mammalian circadian clock: robust synergy of two loops. PLoS Comput. Biol. 7(12), e1002309 (2011)CrossRef Relógio, A., Westermark, P.O., Wallach, T., Schellenberg, K., Kramer, A., Herzel, H.: Tuning the mammalian circadian clock: robust synergy of two loops. PLoS Comput. Biol. 7(12), e1002309 (2011)CrossRef
20.
Zurück zum Zitat Rizk, A., Batt, G., Fages, F., Soliman, S.: A general computational method for robustness analysis with applications to synthetic gene networks. Bioinformatics 12(25), il69–il78 (2009) Rizk, A., Batt, G., Fages, F., Soliman, S.: A general computational method for robustness analysis with applications to synthetic gene networks. Bioinformatics 12(25), il69–il78 (2009)
21.
Zurück zum Zitat Rizk, A., Batt, G., Fages, F., Soliman, S.: Continuous valuations of temporal logic specifications with applications to parameter optimization and robustness measures. Theor. Comput. Sci. 412(26), 2827–2839 (2011)MathSciNetCrossRefMATH Rizk, A., Batt, G., Fages, F., Soliman, S.: Continuous valuations of temporal logic specifications with applications to parameter optimization and robustness measures. Theor. Comput. Sci. 412(26), 2827–2839 (2011)MathSciNetCrossRefMATH
22.
Zurück zum Zitat Traynard, P., Fages, F., Soliman, S.: Trace simplifications preserving temporal logic formulae with case study in a coupled model of the cell cycle and the circadian clock. In: Mendes, P., Dada, J.O., Smallbone, K. (eds.) CMSB 2014. LNCS, vol. 8859, pp. 114–128. Springer, Heidelberg (2014) Traynard, P., Fages, F., Soliman, S.: Trace simplifications preserving temporal logic formulae with case study in a coupled model of the cell cycle and the circadian clock. In: Mendes, P., Dada, J.O., Smallbone, K. (eds.) CMSB 2014. LNCS, vol. 8859, pp. 114–128. Springer, Heidelberg (2014)
23.
Zurück zum Zitat Ünsal-Kaçmaz, K., Mullen, T.E., Kaufmann, W.K., Sancar, A.: Coupling of human circadian and cell cycles by the timeless protein. Mol. Cell. Biol. 25(8), 3109–3116 (2005)CrossRef Ünsal-Kaçmaz, K., Mullen, T.E., Kaufmann, W.K., Sancar, A.: Coupling of human circadian and cell cycles by the timeless protein. Mol. Cell. Biol. 25(8), 3109–3116 (2005)CrossRef
24.
Zurück zum Zitat Weisenberger, D., Scheer, U.: A possible mechanism for the inhibition of ribosomal rna gene transcription during mitosis. J. Cell Biol. 129, 561–575 (1995)CrossRef Weisenberger, D., Scheer, U.: A possible mechanism for the inhibition of ribosomal rna gene transcription during mitosis. J. Cell Biol. 129, 561–575 (1995)CrossRef
Metadaten
Titel
Model-Based Investigation of the Effect of the Cell Cycle on the Circadian Clock Through Transcription Inhibition During Mitosis
verfasst von
Pauline Traynard
François Fages
Sylvain Soliman
Copyright-Jahr
2015
DOI
https://doi.org/10.1007/978-3-319-23401-4_18