Different gene regulation strategies revealed by analysis of binding motifs

Trends Genet. 2009 Oct;25(10):434-40. doi: 10.1016/j.tig.2009.08.003. Epub 2009 Oct 6.


Coordinated regulation of gene expression relies on transcription factors (TFs) binding to specific DNA sites. Our large-scale information-theoretical analysis of > 950 TF-binding motifs demonstrates that prokaryotes and eukaryotes use strikingly different strategies to target TFs to specific genome locations. Although bacterial TFs can recognize a specific DNA site in the genomic background, eukaryotic TFs exhibit widespread, nonfunctional binding and require clustering of sites to achieve specificity. We find support for this mechanism in a range of experimental studies and in our evolutionary analysis of DNA-binding domains. Our systematic characterization of binding motifs provides a quantitative assessment of the differences in transcription regulation in prokaryotes and eukaryotes.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Base Sequence
  • Binding Sites / genetics
  • Eukaryotic Cells / metabolism
  • Gene Expression Regulation*
  • Genome / genetics
  • Models, Genetic
  • Prokaryotic Cells / metabolism
  • Protein Binding
  • Transcription Factors / metabolism*


  • Transcription Factors