Oscillatory regulation of hes1: Discrete stochastic delay modelling and simulation

PLoS Computational Biology

Volumn 2, Issue 9, 2006, Pages 1017-1030

  Barrio, Manuel ^a   Burrage, Kevin ^b   Leier, André ^b   Tian, Hai ^b  

^a UNIVERSITY OF VALLADOLID   (Spain)

^b UNIVERSITY OF QUEENSLAND   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

STOCHASTIC MODELS;

DELAY MODELS; DETERMINISTIC MODELING; DISCRETE STOCHASTIC SIMULATION; EXPRESSION LEVELS; MODEL AND SIMULATION; MOLECULAR SPECIES; OSCILLATORY REGULATIONS; STOCHASTIC DELAY; STOCHASTIC SIMULATION ALGORITHMS; SUSTAINED OSCILLATIONS;

STOCHASTIC SYSTEMS;

TRANSCRIPTION FACTOR HES 1; HOMEODOMAIN PROTEIN; MESSENGER RNA;

ALGORITHM; ARTICLE; CHEMICAL REACTION KINETICS; GENE EXPRESSION; GENETIC TRANSCRIPTION; MOLECULAR MODEL; OSCILLATION; PROTEIN EXPRESSION; REGULATORY MECHANISM; RNA TRANSLATION; SIMULATION; STOCHASTIC MODEL; BIOLOGICAL MODEL; BIOLOGY; COMPUTER SIMULATION; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; MOLECULAR GENETICS; SENSITIVITY AND SPECIFICITY; STATISTICS;

COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; GENE EXPRESSION REGULATION; HOMEODOMAIN PROTEINS; MODELS, BIOLOGICAL; MOLECULAR SEQUENCE DATA; RNA, MESSENGER; SENSITIVITY AND SPECIFICITY; STOCHASTIC PROCESSES;

EID: 33749336242     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.0020117     Document Type: Article

References (22)

1. Reppert SM, Weaver DR (2001) Molecular analysis of mammalian circadian rhythms. Annu Rev Physiol 63: 647-676.
2. Saga Y, Takeda H (2001) The making of the somite: Molecular events in vertebrate segmentation. Nat Rev Genet 2: 835-845.
3. Hirata H, Yoshiura S, Ohtsuka T, Bessho Y, Harada T, et al. (2002) Oscillatory expression of the bHLH factor Hes1 regulated by a negative feedback loop. Science 298: 840-843.
4. Balsalobre A, Damiola F, Schibler U (1998) A serum shock induces circadian gene expression in mammalian tissue culture cells. Cell 93: 929-937.
5. Ström A, Castella P, Rockwood J, Wagner J, Caudy M (1997) Mediation of NGF signaling by post-translational inhibition of HES-1, a basic helix-loop-helix repressor of neuronal differentiation. Genes Dev 11: 3168-3181.
6. Palmeirim I, Henrique D, Ish-Horowicz D, Pourquié O (1997) Avian hairy gene expression identifies a molecular clock linked to vertebrate segmentation and somitogenesis. Cell 91: 639-648.
7. Elowitz MB, Leibler S (2000) A synthetic oscillatory network of transcriptional regulators. Nature 403: 335-338.
8. Monk NAM (2003) Oscillatory expression of Hes1, p53, and NF-κB driven by transcriptional time delays. Curr Biol 13: 1409-1413.
9. Jensen MH, Sneppen K, Tiana G (2003) Sustained oscillations and time delays in gene expression of protein Hes1. FEBS Lett 541: 176-177.
10. Lewis J (2003) Autoinhibition with transcriptional delay: A simple mechanism for the zebrafish somitogenesis oscillator. Curr Biol 13: 1398-1408.
11. Bernard S, Čajavec B, Pujo-Menjouet L, Mackey MC, Herzel H (2006). Modeling transcriptional feedback loops: The role of gro/tle1 in hes1 oscillations. Phil Transact A Math Phys Eng Sci 364: 1155-1170.
12. Goodwin BC (1965) Oscillatory behavior in enzymatic control processes. Adv Enzyme Regul 3: 425-438.
13. an der Heiden U (1979) Delays in physiological systems. J Math Biol 8: 345-364.
14. Gillespie DT (1977) Exact stochastic simulation of coupled chemical reactions. J Phys Chem 81: 2340-2361.
15. Bolouri H, Davidson EH (2003) Transcriptional regulatory cascades in development: Initial rates, not steady state, determine network kinetics. Proc Natl Acad Sci U S A 100: 9371-9376.
16. Arkin A, Ross J, McAdams HH (1998) Stochastic kinetic analysis of developmental pathway bifurcation in phage lambda-infected Escherichia coli cells. Genetics 149: 1633-1648.
17. Gillespie DT (2001) Approximate accelerated stochastic simulation of chemically reacting systems. J Chem Phys 115: 1716-1733.
18. Tian T, Burrage K (2004) Binomial leap methods for simulating stochastic chemical kinetics. J Chem Phys 121: 10356-10364.
19. Haseltine EL, Rawlings JB (2002) Approximate simulation of coupled fast and slow reactions for stochastic chemical kinetics. J Chem Phys 117: 6959-6969.
20. Goutsias J (2005) Quasiequilibrium approximation of fast reaction kinetics in stochastic biochemical systems. J Chem Phys 122: 1-15.
21. Burrage K, Tian T, Burrage P (2004) A multi-scaled approach for simulating chemical reaction systems. Prog Biophys Mol Biol 85: 217-234.
22. Gillespie DT (1991) Markov processes: An introduction for physical scientists. Academic Press. 592 p.