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Background  Gene body methylation at CG dinucleotides is a widely conserved feature of methylated genomes but remains poorly understood. The  Arabidopsis thaliana  strain Cvi has depleted gene body methylation relative to the reference strain Col. Here, we leverage this natural epigenetic difference to investigate gene body methylation stability.    Results  Recombinant inbred lines derived from Col and Cvi were used to examine the transmission of distinct gene body methylation states. The vast majority of genic CG methylation patterns are faithfully transmitted over nine generations according to parental genotype, with only 1–4% of CGs either losing or gaining methylation relative to the parent. Genic CGs that fail to maintain the parental methylation state are shared among independent lines, suggesting that these are not random occurrences. We use a logistic regression framework to identify features that best predict sites that fail to maintain parental methylation state. Intermediate levels of CG methylation around a dynamic CG site and high methylation variability across many  A. thaliana  strains at that site are the strongest predictors. These data suggest that the dynamic CGs we identify are not specific to the Col–Cvi recombinant inbred lines but have an epigenetic state that is inherently less stable within the  A. thaliana  species. Extending this, variably methylated genic CGs in maize and  Brachypodium distachyon  are also associated with intermediate local CG methylation.    Conclusions  These results provide new insights into the features determining the inheritance of gene body methylation and demonstrate that two different methylation equilibria can be maintained within single individuals.    Electronic supplementary material  The online version of this article (doi:10.1186/s13059-017-1206-2) contains supplementary material, which is available to authorized users.

Proximal methylation features associated with nonrandom changes in gene body methylation