To understand their responses to DNA damage, Arabidopsis plants were exposed to methyl methanesulfonate(MMS). Such treatment inhibited growth and decreased the leaf chlorophyll content. A concomitant change in the expression of cell cyclerelated genes also occurred. CYCB1 expression was slightly increased but that of CYCD1 declined. To identify the genetic elements in these responses, genome-wide transcription profiling of Arabidopsis was performed following the MMS treatment, using a cDNA microarray. Expression was altered by more than two-fold for 3666 genes - i.e., 1657 genes showed an increase and 2009 genes had a decrease in transcripts. Five DNA repair-related genes were slightly enhanced, while several disease resistance-related and glutathione transferase genes were strongly up-regulated. Interestingly, 27 ubiquitin-related genes were also altered by more than two-fold, suggesting that protein degradation may have been involved in those damage responses. These microarray results were validated by RT-PCR.