Whole-genome expression analysis of snf/swi mutants of Saccharomyces cerevisiae

The Saccharomyces cerevisiae Snf/Swi complex has been previously demonstrat ed to control transcription and chromatin structure of particular genes in vivo and to remodel nucleosomes in vitro. We have performed whole-genome ex pression analysis, using DNA microarrays, to study mutants deleted for a ge ne encoding one conserved (Snf2) or one unconserved (Swi1) Snf/Swi componen t. This analysis was performed on cells grown in both rich and minimal medi a. The microarray results, combined with Northern blot, computational, and genetic analyses, show that snf2 Delta and swi1 Delta mutations cause simil ar effects on mRNA levels, that Snf/Swi controls some genes differently in rich and minimal media, and that Snf/Swi control is exerted at the revel of individual genes rather than over larger chromosomal domains. In addition, this work shows that Snf/Swi controls mRNA levels of MAT alpha-specific ge nes, likely via controlling transcription of the regulators MAT alpha 1 and MCM1. Finally, we provide evidence that Snf/Swi acts both as an activator and as a repressor of transcription, and that neither mode of control is an indirect effect of the other.