Eukaryotic cells respond to DNA damage by activating damage checkpoint pathways, which arrest cell cycle progression and induce gene expression. In order to understand how damage checkpoints control the expression of DNA damage-inducible genes, the transcript level of two closely clustered genes, MAG1 and DDI1, was examined in a number of checkpoint mutants. We previously reported that MAG1 induction was abolished in pol2 and rad53 mutants, but not in the mec1-1 mutant. In this study, we found that mec1Delta and dun1Delta null mutants were defective in MAG1 induction, suggesting that MAG1 shares a common regulatory pathway with the RNR1,2,3,4 genes, which are also regulated by the POL2-MEC1-RAD53-DUN1 checkpoint pathway, and that the mec1-1 mutation probably represents a separation-of-function mutation. However, MAG1 is not activated in precisely the same way as the RNR genes, since mutations in CRT1, TUP1 and SSN6, which encode repressors of RNR genes, did not affect basal or induced expression of MAG1. In contrast, the DDI1 transcript level was not affected by any of the above checkpoint mutations. Interestingly, simultaneous inactivation of RAD53 or DUN1 with PDS1, a newly identified checkpoint gene, resulted in severe down-regulation of DDI1 expression, suggesting that DDI1 is controlled by two damage checkpoint pathways, one mediated by POL2-MEC1-RAD53-DUN1 and the other by CHK1-PDS1. On the other hand, deletion of TEL1, a structural homologue of MEC1, did not affect expression of MAG1, DDI1 or RNR3, suggesting that TEL1 plays no role in induction by DNA damage. Based on these and previous studies, we present a model for the role of checkpoint genes in transcriptional regulation in response to DNA damage.