Ectopic hypermethylation of flower-specific genes in Arabidopsis

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.