Mutations in the SUPERMAN gene affect flower development in Arabidopsi
s. Seven heritable but unstable sup epi-alleles (the clark kent allele
s) are associated with nearly identical patterns of excess cytosine me
thylation within the SUP gene and a decreased level of SUP RNA. Revert
ants of these alleles are largely demethylated at the SUP locus and ha
ve restored levels of SUP RNA. A transgenic Arabidopsis line carrying
an antisense methyltransferase gene, which shows an overall decrease i
n genomic cytosine methylation, also contains a hypermethylated sup al
lele. Thus, disruption of methylation systems may yield more complex o
utcomes than expected and can result in methylation defects at known g
enes. The clark kent alleles differ from the antisense line because th
ey do not show a general decrease in genomic methylation.