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Cytosine methylation is widely known for its role in silencing transposable elements and some genes in plants and mammals. However, whereas methylation of promoter sequences can lead to transcriptional repression, the function of gene body methylation remains elusive. This situation is particularly perplexing in the plant Arabidopsis, where many genes are methylated, specifically, over their body. A new study in this issue of The EMBO Journal shows that gene body methylation results from two conflicting activities, one imposing it at CG sites, and one preventing its extension to CHG sites (where H=A,T or C). Importantly, the latter activity is not targeted towards silent transposable elements and is likely coupled to transcription elongation, suggesting that CHG methylation hinders this step.

Gene body DNA methylation in plants: a means to an end or an end to a means?