The Wassilewskija strain of Arabidopsis has four genes encoding the tryptophan enzyme phosphoribosylanthranilate isomerase (PAI) located at three unlinked sites. These four PAI genes are methylated over their regions of DNA homology. When PAI copy number is reduced by deletion of two tandemly arrayed genes (MePAI1-PAI4), a mutant with fluorescent, tryptophan-deficient phenotypes results, because the two remaining methylated PAI genes (MePAI2 and MePAI3) supply insufficient PAI activity. These two methylated genes can be inherited through meiosis, even when they are segregated away from each other in crosses to a strain with unmethylated PAI genes. However, the mutant phenotypes conferred by the methylated PAI genes are unstable, and mutant plants yield occasional revertant somatic sectors and progeny. Revertant lines display coordinately reduced methylation of both PAI2 and PAI3, implying that this hypomethylation acts in a concerted manner across the genome rather than at individual sites.