title: Phylogeny based discovery of regulatory elements.
abstract: BACKGROUND
  Algorithms that locate evolutionarily conserved sequences have become powerful tools for finding functional DNA elements, including transcription factor binding sites; however, most methods do not take advantage of an explicit model for the constrained evolution of functional DNA sequences.
  
  
  RESULTS
  We developed a probabilistic framework that combines an HKY85 model, which assigns probabilities to different base substitutions between species, and weight matrix models of transcription factor binding sites, which describe the probabilities of observing particular nucleotides at specific positions in the binding site. The method incorporates the phylogenies of the species under consideration and takes into account the position specific variation of transcription factor binding sites. Using our framework we assessed the suitability of alignments of genomic sequences from commonly used species as substrates for comparative genomic approaches to regulatory motif finding. We then applied this technique to Saccharomyces cerevisiae and related species by examining all possible six base pair DNA sequences (hexamers) and identifying sequences that are conserved in a significant number of promoters. By combining similar conserved hexamers we reconstructed known cis-regulatory motifs and made predictions of previously unidentified motifs. We tested one prediction experimentally, finding it to be a regulatory element involved in the transcriptional response to glucose.
  
  
  CONCLUSIONS
  The experimental validation of a regulatory element prediction missed by other large-scale motif finding studies demonstrates that our approach is a useful addition to the current suite of tools for finding regulatory motifs.
authors.affiliation: Department of Genetics, Washington University School of Medicine, 4444 Forest Park Parkway, St. Louis, MO 63108, USA. jgertz@genetics.wustl.edu
authors.forename: Jason
authors.initials: J
authors.lastname: Gertz
authors.forename: Justin C
authors.initials: JC
authors.lastname: Fay
authors.forename: Barak A
authors.initials: BA
authors.lastname: Cohen
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D017124:Conserved Sequence / Q000235:genetics; D008969:Molecular Sequence Data; D010802:Phylogeny; D050436:Regulatory Elements, Transcriptional / Q000235:genetics*; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012689:Sequence Homology, Nucleic Acid; D014157:Transcription Factors / Q000235:genetics*
chemical_list: D014157:Transcription Factors