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

Different gene regulation strategies revealed by analysis of binding motifs.

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  • 1Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.


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.

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