FINDING DNA REGULATORY MOTIFS WITHIN UNALIGNED NONCODING SEQUENCES CLUSTERED BY WHOLE-GENOME MESSENGER-RNA QUANTITATION

Whole-genome mRNA quantitation can be used to identify the genes that are most responsive to environmental or genotypic change. By searching for mutually similar DNA elements among the upstream noncoding DNA se quences of these genes, we can identify candidate regulatory motifs an d corresponding candidate sets of coregulated genes. We have tested th is strategy by applying it to three extensively studied regulatory sys tems in the yeast Saccharomyces cerevisiae: galactose response, heat s hock, and mating type. Galactose-response data yielded the known bindi ng site of Gal4, and six of nine genes known to be induced by galactos e. Heat shock data yielded the cell-cycle activation motif, which is k nown to mediate cell-cycle dependent activation, and a set of genes co ding for all four nucleosomal proteins. Mating type alpha and a data y ielded all of the four relevant DNA motifs and most of the known a- an d alpha-specific genes.