Background: Arabidopsis mutations causing genome-wide hypomethylation are v
iable but display a number of specific developmental abnormalities, includi
ng some that resemble known floral homeotic mutations. We previously showed
that one of the developmental abnormalities present in an antisense-METHYL
TRANSFERASEI (METI) transgenic line resulted from ectopic hypermethylation
of the SUPERMAN gene.
Results: Here, we investigate the extent to which hypermethylation of SUPER
MAN occurs in several hypomethylation mutants, and describe methylation eff
ects at a second gene, AGAMOUS. SUPERMAN gene hypermethylation occurred at
a high frequency in several mutants that cause overall decreases in genomic
DNA methylation. The hypermethylation pattern was largely similar in the d
ifferent mutant backgrounds. Genetic analysis suggests that hypermethylatio
n most likely arose either during meiosis or somatically in small sectors o
f the plant. A second floral development gene, AGAMOUS, also became hyperme
thylated and silenced in an Arabidopsis antisense-METI line.
Conclusions: These results suggest that ectopic hypermethylation of specifi
c genes in mutant backgrounds that show overall decreases in methylation ma
y be a widespread phenomenon that could explain many of the developmental d
efects seen in Arabidopsis methylation mutants. This resembles a phenomenon
seen in cancer cells, which can simultaneously show genome-wide hypomethyl
ation and hypermethylation of specific genes. Comparison of the methylated
sequences in SUPERMAN and AGAMOUS suggests that hypermethylation could invo
lve DNA secondary structures formed by pyrimidine-rich sequences.