Finding functional features in Saccharomyces genomes by phylogenetic footprinting.
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.
Cliften
Paul
P
Department of Genetics, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO 63110, USA.
Sudarsanam
Priya
P
Desikan
Ashwin
A
Fulton
Lucinda
L
Fulton
Bob
B
Majors
John
J
Waterston
Robert
R
Cohen
Barak A
BA
Johnston
Mark
M
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
D021901:DNA, Intergenic; D014157:Transcription Factors