title: Finding functional features in Saccharomyces genomes by phylogenetic footprinting.
abstract: The sifting and winnowing of DNA sequence that occur during evolution cause nonfunctional sequences to diverge, leaving phylogenetic footprints of functional sequence elements in comparisons of genome sequences. We searched for such footprints among the genome sequences of six Saccharomyces species and identified potentially functional sequences. Comparison of these sequences allowed us to revise the catalog of yeast genes and identify sequence motifs that may be targets of transcriptional regulatory proteins. Some of these conserved sequence motifs reside upstream of genes with similar functional annotations or similar expression patterns or those bound by the same transcription factor and are thus good candidates for functional regulatory sequences.
authors.affiliation: Department of Genetics, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO 63110, USA.
authors.forename: Paul
authors.initials: P
authors.lastname: Cliften
authors.forename: Priya
authors.initials: P
authors.lastname: Sudarsanam
authors.forename: Ashwin
authors.initials: A
authors.lastname: Desikan
authors.forename: Lucinda
authors.initials: L
authors.lastname: Fulton
authors.forename: Bob
authors.initials: B
authors.lastname: Fulton
authors.forename: John
authors.initials: J
authors.lastname: Majors
authors.forename: Robert
authors.initials: R
authors.lastname: Waterston
authors.forename: Barak A
authors.initials: BA
authors.lastname: Cohen
authors.forename: Mark
authors.initials: M
authors.lastname: Johnston
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D001665:Binding Sites; D019295:Computational Biology; D017124:Conserved Sequence; D021901:DNA, Intergenic; D020869:Gene Expression Profiling; D005800:Genes, Fungal; D016681:Genome, Fungal; D008969:Molecular Sequence Data; D010802:Phylogeny; D012045:Regulatory Sequences, Nucleic Acid; D012440:Saccharomyces / Q000145:classification / Q000235:genetics* / Q000502:physiology; D012441:Saccharomyces cerevisiae / Q000235:genetics / Q000502:physiology; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D014157:Transcription Factors / Q000378:metabolism
chemical_list: D021901:DNA, Intergenic; D014157:Transcription Factors