Degree dependence in rates of transcription factor evolution explains the unusual structure of transcription networks

Alexander J Stewart, Robert M Seymour, Andrew Pomiankowski

Research output: Contribution to journalArticlepeer-review

10 Citations (Scopus)

Abstract

Transcription networks have an unusual structure. In both prokaryotes and eukaryotes, the number of target genes regulated by each transcription factor, its out-degree, follows a broad tailed distribution. By contrast, the number of transcription factors regulating a target gene, its in-degree, follows a much narrower distribution, which has no broad tail. We constructed a model of transcription network evolution through trans- and cis-mutations, gene duplication and deletion. The effects of these different evolutionary processes on the network structure are enough to produce an asymmetrical in- and out-degree distribution. However, the parameter values required to replicate known in- and out-degree distributions are unrealistic. We then considered variation in the rate of evolution of a gene dependent upon its position in the network. When transcription factors with many regulatory interactions are constrained to evolve more slowly than those with few interactions, the details of the in- and out-degree distributions of transcription networks can be fully reproduced over a range of plausible parameter values. The networks produced by our model depend on the relative rates of the different evolutionary processes. By determining the circumstances under which the networks with the correct degree distributions are produced, we are able to assess the relative importance of the different evolutionary processes in our model during evolution.

Original languageEnglish
Pages (from-to)2493-501
Number of pages9
JournalProceedings. Biological sciences
Volume276
Issue number1666
DOIs
Publication statusPublished - 7 Jul 2009

Keywords

  • Binding Sites
  • Evolution, Molecular
  • Gene Deletion
  • Gene Duplication
  • Gene Expression Regulation
  • Models, Genetic
  • Mutation
  • Transcription Factors/chemistry

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