Methylation interactions in <i>Arabidopsis</i> hybrids require RNA-directed DNA methylation and are influenced by genetic variation

Significance The epigenome influences gene regulation and genome evolution. The DNA methylomes of Arabidopisis hybrids are distinct from both parents; however, how the parental methylomes interact in hybrids is poorly understood. We discovered pervasive, nonadditive DNA methylation changes (“methylation interactions”) throughout the genome in hybrids of Col and C24 Arabidopsis accessions. Methylation interactions correlated with high levels of small interfering RNAs, known components of the RNA-directed DNA methylation (RdDM) pathway. Indeed, abrogation of RdDM activity abolished methylation interactions in filial 1 (F1) hybrids. Methylation interactions have distinct polymorphism frequencies: Regions with increased methylation compared with the parents are highly conserved, whereas regions with decreased methylation are divergent. Our results show that RdDM is required for DNA methylation interactions in hybrids.