In Arabidopsis a SWI2/SNF2 chromatin remodeling factor-related protein DDM1 and 
a cytosine methyltransferase MET1 are required for maintenance of genomic 
cytosine methylation. Mutations in either gene cause global demethylation. In 
this work we have assessed the effects of these mutations on the PAI tryptophan 
biosynthetic gene family, which consists of four densely methylated genes 
arranged as a tail-to-tail inverted repeat plus two unlinked singlet genes. The 
methylation mutations caused only partial demethylation of the PAI loci: ddm1 
had a strong effect on the singlet genes but a weaker effect on the inverted 
repeat, whereas met1 had a stronger effect on the inverted repeat than on the 
singlet genes. The double ddm1 met1 mutant also displayed partial demethylation 
of the PAI genes, with a pattern similar to the ddm1 single mutant. To determine 
the relationship between partial methylation and expression for the singlet PAI2 
gene we constructed a novel reporter strain of Arabidopsis in which PAI2 
silencing could be monitored by a blue fluorescent plant phenotype diagnostic of 
tryptophan pathway defects. This reporter strain revealed that intermediate 
levels of methylation correlate with intermediate suppression of the fluorescent 
phenotype.