Finding Functional Features in Saccharomyces Genomes by Phylogenetic Footprinting

• Published in: Science (American Association for the Advancement of Science) Vol. 301; no. 5629; pp. 71 - 76
• Main Authors: Cliften, Paul, Sudarsanam, Priya, Desikan, Ashwin, Fulton, Lucinda, Fulton, Bob, Majors, John, Waterston, Robert, Cohen, Barak A., Johnston, Mark
• Format: Journal Article
• Language: English
• Published: Washington, DC American Association for the Advancement of Science 04.07.2003; The American Association for the Advancement of Science
• Subjects: Algorithms; Analysis; Base Sequence; Binding Sites; Biological and medical sciences; Cell cycle; Coding; Comparative Analysis; Computational Biology; Conserved Sequence; Conserved sequences; DNA damage; DNA, Intergenic; Evolution; Fundamental and applied biological sciences. Psychology; Gene Expression Profiling; Genes; Genes, Fungal; Genetic aspects; Genome, Fungal; Genomes; Genomics; Intergenic DNA; Molecular and cellular biology; Molecular Sequence Data; Motifs; Open reading frames; Phylogeny; Regulatory Sequences, Nucleic Acid; Saccharomyces; Saccharomyces - classification; Saccharomyces - genetics; Saccharomyces - physiology; Saccharomyces cerevisiae - genetics; Saccharomyces cerevisiae - physiology; Sequence Alignment; Sequence Analysis, DNA; Transcription factors; Transcription Factors - metabolism; Yeast; United States; Genetics
• ISSN: 0036-8075; 1095-9203
• DOI: 10.1126/science.1084337

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.