Reconstructing a network of stress-response regulators via dynamic system modeling of gene regulation

Wei Sheng Wu, Wen Hsiung Li, Bor Sen Chen

Research output: Contribution to journalArticle

5 Citations (Scopus)

Abstract

Unicellular organisms such as yeasts have evolved mechanisms to respond to environmental stresses by rapidly reorganizing the gene expression program. Although many stress-response genes in yeast have been discovered by DNA microarrays, the stress-response transcription factors (TFs) that regulate these stress-response genes remain to be investigated. In this study, we use a dynamic system model of gene regulation to describe the mechanism of how TFs may control a gene's expression. Then, based on the dynamic system model, we develop the Stress Regulator Identification Algorithm (SRIA) to identify stress-response TFs for six kinds of stresses. We identified some general stress-response TFs that respond to various stresses and some specific stress-response TFs that respond to one specific stress. The biological significance of our findings is validated by the literature. We found that a small number of TFs is probably sufficient to control a wide variety of expression patterns in yeast under different stresses. Two implications can be inferred from this observation. First, the response mechanisms to different stresses may have a bow-tie structure. Second, there may be regulatory cross-talks among different stress responses. In conclusion, this study proposes a network of stress-response regulators and the details of their actions.

Original languageEnglish
Pages (from-to)53-62
Number of pages10
JournalGene Regulation and Systems Biology
Volume2008
Issue number2
DOIs
Publication statusPublished - 2008 Jan 1

All Science Journal Classification (ASJC) codes

  • Ecology, Evolution, Behavior and Systematics
  • Molecular Biology
  • Genetics
  • Computer Science Applications

Fingerprint Dive into the research topics of 'Reconstructing a network of stress-response regulators via dynamic system modeling of gene regulation'. Together they form a unique fingerprint.

  • Cite this