Stochastic simulation of the mammalian circadian clock

Daniel B. Forger, Charles Peskin

Research output: Contribution to journalArticle

Abstract

Circadian (nearly 24-h) clocks are remarkably accurate at timing biological events despite the randomness of their biochemical reactions. Here we examine the causes of their immunity to molecular noise in the context of a detailed stochastic mathematical model of the mammalian circadian clock. This stochastic model is a direct generalization of the deterministic mammalian circadian clock model previously developed. A feature of that model is that it completely specifies all molecular reactions, leaving no ambiguity in the formulation of a stochastic version of the model. With parameters based on experimental data concerning clock protein concentrations within a cell, we find accurate circadian rhythms in our model only when promoter interaction occurs on the time scale of seconds. As the model is scaled up by proportionally increasing the numbers of molecules of all species and the reaction rates with the promoter, the observed variability scales as 1/n0.5, where n is the number of molecules of any species. Our results show that gene duplication increases robustness by providing more promoters with which the transcription factors of the model can interact. Although PER2 mutants were not rhythmic in the deterministic version of this model, they are rhythmic in the stochastic version.

Original languageEnglish (US)
Pages (from-to)321-324
Number of pages4
JournalProceedings of the National Academy of Sciences of the United States of America
Volume102
Issue number2
DOIs
StatePublished - Jan 11 2005

Fingerprint

Circadian Clocks
Gene Duplication
Circadian Rhythm
Noise
Immunity
Transcription Factors
Theoretical Models
Proteins

Keywords

  • Eukaryotic transcription regulation
  • Gillespie method
  • Mathematical models
  • Molecular noise
  • Phosphorylation

ASJC Scopus subject areas

  • Genetics
  • General

Cite this

Stochastic simulation of the mammalian circadian clock. / Forger, Daniel B.; Peskin, Charles.

In: Proceedings of the National Academy of Sciences of the United States of America, Vol. 102, No. 2, 11.01.2005, p. 321-324.

Research output: Contribution to journalArticle

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