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In paramutation two alleles of a gene interact so that one of the alleles is epigenetically silenced. The silenced state is then genetically transmissible for many generations. The large (220 kbp) multigenic complex R-r is paramutable: its level of expression is changed during paramutation. R-r was found to exhibit increases in its level of cytosine methylation (C-methylation) following paramutation. These C-methylation changes are localized to the 5′ portions of the two genes in the complex that are most sensitive to paramutation. These methylation changes flank a small region called σ that is thought to have been derived from a transposon named doppia. A mutant derivative of R-r that has a deletion of the σ region fails to become methylated under conditions in which R-r is heavily methylated. This suggests that the presence of σ sequences at the locus is required for the methylation changes that are observed following paramutation.

Paramutation of the r1 Locus of Maize Is Associated With Increased Cytosine Methylation