Global response of Saccharomyces cerevisiae to an alkylating agent

DNA chip technology enables simultaneous examination of how approximate to 6,200 Saccharomyces cerevisiae gene transcript levels, representing the ent ire genome, respond to environmental change. By using chips bearing oligonu cleotide arrays, we show that, after exposure to the alkylating agent methy l methanesulfonate, approximate to 325 gene transcript levels are increased and approximate to 76 are decreased. Of the 21 genes that already were kno wn to be induced by a DNA-damaging agent, 18 can be scored as inducible in this data set, and surprisingly, most of the newly identified inducible gen es are induced even more strongly than these 18. We examined 42 responsive and 8 nonresponsive ORFs by conventional Northern blotting, and 48 of these 50 ORFs responded as they did by DNA chip analysis, with magnitudes displa ying a correlation coefficient of 0.79. Responsive genes fail into several expected and many unexpected categories. Evidence for the induction of a pr ogram to eliminate and replace alkylated proteins is presented.