The co-regulation mechanism of transcription factors in the human gene regulatory network

Nucleic Acids Res. 2012 Oct;40(18):8849-61. doi: 10.1093/nar/gks664. Epub 2012 Jul 13.

Abstract

The co-regulation of transcription factors (TFs) has been widely observed in various species. Why is such a co-regulation mechanism needed for transcriptional regulation? To answer this question, the following experiments and analyses were performed. First, examination of the human gene regulatory network (GRN) indicated that co-regulation was significantly enriched in the human GRN. Second, mathematical simulation of an artificial regulatory network showed that the co-regulation mechanism was related to the biphasic dose-response patterns of TFs. Third, the relationship between the co-regulation mechanism and the biphasic dose-response pattern was confirmed using microarray experiments examining different time points and different doses of the toxicant tetrachlorodibenzodioxin. Finally, two mathematical models were constructed to mimic highly co-regulated networks (HCNs) and little co-regulated networks (LCNs), and we found that HCNs were more robust to parameter perturbation than LCNs, whereas LCNs were faster in adaptation to environmental changes than HCNs.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Cell Line, Tumor
  • Evolution, Molecular
  • Gene Expression Regulation*
  • Gene Regulatory Networks*
  • Humans
  • Models, Genetic
  • Signal Transduction / genetics
  • Transcription Factors / metabolism*

Substances

  • Transcription Factors