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PHYLOGENETIC ASSOCIATION MAPPING

DNA methylation makes mutational history

Nature Plants volume 5, pages 772–773 (2019)Cite this article

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A quantitative phylogenetic association mapping approach links genic mutational spectra to the evolution of DNA methylation in the Brassicaceae family of flowering plants. The method has wider applications and may usher in a new era in our understanding of species diversity.

Cytosine methylation is an important epigenetic modification and a pervasive feature of eukaryotic genomes. Plants methylate cytosines in three sequence contexts: CG, CHG and CHH (where ‘H’ refers to either A, T or C nucleotides). Dense cytosine methylation is found mainly in transposable elements and repeat sequences. But an enrichment for methylated CG dinucleotides can also be seen in a subset of genes, a phenomenon termed ‘gene body methylation’ (gbM). These genes appear to be evolutionary important1,2,3 and display distinct expression profiles4,5. Curiously, unlike in transposable elements where cytosine methylation acts as a transcriptional repressor, the regulatory role of gbM remains elusive6. Experimental removal of gbM seems to have little impact on gene expression7, suggesting that it is ‘just a by-product’ of a yet unknown process, possibly even unrelated to transcription. Whatever its function, the evolutionary benefits of gbM must outweigh its mutagenic potential8. Indeed, methylated cytosines transition to thyamines (C-to-T) at a higher rate than unmethylated cytosines, with potentially deleterious effects. That plants have been willing to take that risk is illustrated by Willing et al.9 in the current issue of Nature Plants. The authors go back in time and show how the mutational spectrum of genes has been shaped by the evolution of gbM.

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Fig. 1: CMT3-mediated evolution of gbM shapes the mutational spectrum of genes.

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Authors and Affiliations

  1. Department of Plant Sciences, Technical University of Munich, Freising, Germany

    Frank Johannes

  2. Institute for Advanced Study, Technical University of Munich, Garching, Germany

    Frank Johannes

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  1. Frank Johannes
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Correspondence to Frank Johannes.

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Johannes, F. DNA methylation makes mutational history. Nat. Plants 5, 772–773 (2019). https://doi.org/10.1038/s41477-019-0491-z

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