Transcriptional stochasticity in gene expression

Tomasz Lipniacki, Pawel Paszek, Anna Marciniak-Czochra, Allan R. Brasier, Marek Kimmel

Research output: Contribution to journalArticle

79 Citations (Scopus)

Abstract

Due to the small number of copies of molecular species involved, such as DNA, mRNA and regulatory proteins, gene expression is a stochastic phenomenon. In eukaryotic cells, the stochastic effects primarily originate in regulation of gene activity. Transcription can be initiated by a single transcription factor binding to a specific regulatory site in the target gene. Stochasticity of transcription factor binding and dissociation is then amplified by transcription and translation, since target gene activation results in a burst of mRNA molecules, and each mRNA copy serves as a template for translating numerous protein molecules. In the present paper, we explore a mathematical approach to stochastic modeling. In this approach, the ordinary differential equations with a stochastic component for mRNA and protein levels in a single cells yield a system of first-order partial differential equations (PDEs) for two-dimensional probability density functions (pdf). We consider the following examples: Regulation of a single auto-repressing gene, and regulation of a system of two mutual repressors and of an activator-repressor system. The resulting PDEs are approximated by a system of many ordinary equations, which are then numerically solved.

Original languageEnglish (US)
Pages (from-to)348-367
Number of pages20
JournalJournal of Theoretical Biology
Volume238
Issue number2
DOIs
StatePublished - Jan 21 2006

Fingerprint

Stochasticity
Gene expression
Messenger RNA
Gene Expression
Genes
Gene
gene expression
Transcription factors
Transcription
Transcription Factor
Proteins
Protein
Partial differential equations
Transcription Factors
transcription factors
Partial differential equation
transcription (genetics)
Molecules
Target
gene activation

Keywords

  • Gene regulation
  • Probability density function
  • Stochasticity
  • Transcription
  • Transport-type equations

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)

Cite this

Lipniacki, T., Paszek, P., Marciniak-Czochra, A., Brasier, A. R., & Kimmel, M. (2006). Transcriptional stochasticity in gene expression. Journal of Theoretical Biology, 238(2), 348-367. https://doi.org/10.1016/j.jtbi.2005.05.032

Transcriptional stochasticity in gene expression. / Lipniacki, Tomasz; Paszek, Pawel; Marciniak-Czochra, Anna; Brasier, Allan R.; Kimmel, Marek.

In: Journal of Theoretical Biology, Vol. 238, No. 2, 21.01.2006, p. 348-367.

Research output: Contribution to journalArticle

Lipniacki, T, Paszek, P, Marciniak-Czochra, A, Brasier, AR & Kimmel, M 2006, 'Transcriptional stochasticity in gene expression', Journal of Theoretical Biology, vol. 238, no. 2, pp. 348-367. https://doi.org/10.1016/j.jtbi.2005.05.032
Lipniacki T, Paszek P, Marciniak-Czochra A, Brasier AR, Kimmel M. Transcriptional stochasticity in gene expression. Journal of Theoretical Biology. 2006 Jan 21;238(2):348-367. https://doi.org/10.1016/j.jtbi.2005.05.032
Lipniacki, Tomasz ; Paszek, Pawel ; Marciniak-Czochra, Anna ; Brasier, Allan R. ; Kimmel, Marek. / Transcriptional stochasticity in gene expression. In: Journal of Theoretical Biology. 2006 ; Vol. 238, No. 2. pp. 348-367.
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