Cis-acting sites contributing to expression of divergently transcribed DAL1 and DAL4 genes in S-cerevisiae: a word of caution when correlating cis-acting sequences with genome-wide expression analyses

Correlating genome-wide expression profiles with sequence searches of promo ter regions is being used as a technique to identify putative binding sites for transacting factors or to refine consensus sequences of those already known. To evaluate the limitations of such an approach in our studies of GA TA-mediated transcription in Saccharomyces cerevisiae, we identified the: r elative contributions made to DAL1 and DAL4 expression by each of five Gln3 p-, and/or Gat1p-, and three Dal82p-binding site homologous sequences situa ted in the 829-bp intergenic region separating these highly related, diverg ently transcribed genes. Our data suggest that although the correlation of repeated sequences or sequence homologies appearing within promoter regions with expression profiles obtained from genome-wide transcription analyses can provide useful starting points for analyses of cis-acting sites, signif icant limitations and possibilities for misinterpretation also abound.