title: Different gene regulation strategies revealed by analysis of binding motifs.
abstract: 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.
authors.affiliation: Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.
authors.forename: Zeba
authors.initials: Z
authors.lastname: Wunderlich
authors.forename: Leonid A
authors.initials: LA
authors.lastname: Mirny
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D001665:Binding Sites / Q000235:genetics; D005057:Eukaryotic Cells / Q000378:metabolism; D005786:Gene Expression Regulation; D016678:Genome / Q000235:genetics; D008957:Models, Genetic; D011387:Prokaryotic Cells / Q000378:metabolism; D011485:Protein Binding; D014157:Transcription Factors / Q000378:metabolism*
chemical_list: D014157:Transcription Factors