Genome-Wide Evolutionary Analysis of Eukaryotic DNA Methylation

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Science  15 Apr 2010:
DOI: 10.1126/science.1186366


Eukaryotic cytosine methylation represses transcription, but also occurs in the bodies of active genes, and the extent of methylation biology conservation is unclear. Here, we quantify DNA methylation in 17 eukaryotic genomes and find that gene body methylation is conserved between plants and animals, whereas selective methylation of transposons is not. We show that methylation of plant transposons in the CHG context extends to green algae, and present evidence for RNA-directed DNA methylation of fungal genes. Exclusion of histone H2A.Z from methylated DNA is conserved between plants and animals. Our data demonstrate that extant DNA methylation systems are mosaics of conserved and derived features, and indicate that gene body methylation is an ancient property of eukaryotic genomes.