title: Functional trends in structural classes of the DNA binding domains of regulatory transcription factors.
abstract: The DNA-binding domain (DBD) structure of a regulatory transcription factor (TF) is important in determining its DNA sequence specificity, but it is unclear whether a relationship exists between DBD structure and general TF biological function or regulatory mechanism. We observed moderate enrichment of functional annotation terms among TFs of the same structural class in Escherichia coli, Saccharomyces cerevisiae, Drosophila melanogaster, or Mus musculus, suggesting some preference for TFs of similar structures in the regulation of similar processes. In yeast, we also found trends among TF structural classes in phenomena including gene expression coherence, DNA binding site motif similarity, the general or specific nature of TFs' regulatory roles, and the position of a TF in a gene regulatory network. These results suggest that the biophysical constraints of different TF structural classes play a role in their gene regulatory mechanisms.
authors.affiliation: Division of Genetics, Department of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA 02115, USA. rpmccord@fas.harvard.edu
authors.forename: Rachel Patton
authors.initials: RP
authors.lastname: McCord
authors.forename: Martha L
authors.initials: ML
authors.lastname: Bulyk
mesh_terms: D000818:Animals; D001665:Binding Sites; D055592:Biophysical Phenomena; D001703:Biophysics; D019295:Computational Biology; D004247:DNA / Q000235:genetics / Q000378:metabolism*; D030562:Databases, Protein; D029721:Drosophila Proteins / Q000737:chemistry / Q000145:classification / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000737:chemistry / Q000145:classification / Q000378:metabolism; D005786:Gene Expression Regulation; D051379:Mice; D008954:Models, Biological; D017434:Protein Structure, Tertiary; D029701:Saccharomyces cerevisiae Proteins / Q000737:chemistry / Q000145:classification / Q000378:metabolism; D014157:Transcription Factors / Q000737:chemistry* / Q000145:classification* / Q000378:metabolism
chemical_list: D029721:Drosophila Proteins; D029968:Escherichia coli Proteins; D029701:Saccharomyces cerevisiae Proteins; D014157:Transcription Factors; D004247:DNA