Surveying Saccharomyces genomes to identify functional elements by comparative DNA sequence analysis

Comparative sequence analysis has facilitated the discovery of protein codi ng genes and important functional sequences within proteins, but has been l ess useful for identifying functional sequence elements in nonprotein-codin g DNA because the relatively rapid rate of change of nonprotein-coding sequ ences and the relative simplicity of non-coding regulatory sequence element s necessitates the comparison of sequences of relatively closely related sp ecies. We tested the use of comparative DNA sequence analysis to aid identi fication of promoter regulatory elements, nonprotein-coding RNA genes, and small protein-coding genes by surveying random DNA sequences of several Sac charomyces yeast species, with the goal of learning which species are best suited for comparisons with S. cerevisiae. We also determined the DNA seque nce of a few specific promoters and RNA genes of several Saccharomyces spec ies to determine the degree of conservation of known Functional elements wi thin the genome. Our results lead us to conclude that comparative DNA seque nce analysis will enable identification of functionally conserved elements within the yeast genome, and suggest a path for obtaining this information.