DNA sequence properties that predict susceptibility to epiallelic switching

Transgenerationally heritable epialleles are defined by the stable propagation of alternative transcriptional states through mitotic and meiotic cell cycles. Given that the propagation of DNA methylation at CpG sites, mediated in Arabidopsis by MET1, plays a central role in epigenetic inheritance, we examined genome-wide DNA methylation in partial and complete loss-of-function met1 mutants. We interpreted the data in relation to transgenerational epiallelic stability and provide evidence that DNA sequence features such as density of CpGs and genomic repetitiveness can be used to predict susceptibility to epiallelic switching. The importance of these rules was confirmed by analyses of common epialleles in natural Arabidopsis accessions and verified in rice.