Finding functional features in Saccharomyces genomes by phylogenetic footprinting

Science. 2003 Jul 4;301(5629):71-6. doi: 10.1126/science.1084337. Epub 2003 May 29.


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.

Publication types

  • Comparative Study
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Algorithms
  • Base Sequence
  • Binding Sites
  • Computational Biology
  • Conserved Sequence*
  • DNA, Intergenic*
  • Gene Expression Profiling
  • Genes, Fungal
  • Genome, Fungal*
  • Molecular Sequence Data
  • Phylogeny*
  • Regulatory Sequences, Nucleic Acid*
  • Saccharomyces / classification
  • Saccharomyces / genetics*
  • Saccharomyces / physiology
  • Saccharomyces cerevisiae / genetics
  • Saccharomyces cerevisiae / physiology
  • Sequence Alignment
  • Sequence Analysis, DNA
  • Transcription Factors / metabolism


  • DNA, Intergenic
  • Transcription Factors