Catching transcriptional regulation by thermostatistical modeling

Till D. Frank, Alex Cheong, Mariko Okada-Hatakeyama, Boris N. Kholodenko

Research output: Contribution to journalArticlepeer-review

Abstract

Gene expression is frequently regulated by multiple transcription factors (TFs). Thermostatistical methods allow for a quantitative description of interactions between TFs, RNA polymerase and DNA, and their impact on the transcription rates. We illustrate three different scales of the thermostatistical approach: the microscale of TF molecules, the mesoscale of promoter energy levels and the macroscale of transcriptionally active and inactive cells in a cell population. We demonstrate versatility of combinatorial transcriptional activation by exemplifying logic functions, such as AND and OR gates. We discuss a metric for cell-to-cell transcriptional activation variability known as Fermi entropy. Suitability of thermostatistical modeling is illustrated by describing the experimental data on transcriptional induction of NF?B and the c-Fos protein.
Original languageEnglish
Article number045007
Number of pages11
JournalPhysical Biology
Volume9
Issue number4
DOIs
Publication statusPublished - Aug 2012

Bibliographical note

© 2012 IOP Publishing Ltd

Keywords

  • algorithms
  • animals
  • computer simulation
  • entropy
  • fuzzy logic
  • humans
  • genetic models
  • statistical models
  • NF-kappa B
  • genetic promoter regions
  • proto-oncogene proteins c-fos
  • transcription factors
  • transcriptional activation

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