Genome-Wide Evolutionary Analysis of Eukaryotic DNA Methylation

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Science  14 May 2010:
Vol. 328, Issue 5980, pp. 916-919
DOI: 10.1126/science.1186366

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Epigenetic Maps

Methylation of genomic DNA on cytosine bases provides critical epigenetic regulation of gene expression and is involved in silencing transposable elements (TEs) and repeated sequences, as well as regulating imprinted gene expression. Zemach et al. (p. 916, published online 15 April; see the Perspective by Jeltsch) analyzed DNA methylation in the genomes of five plants, five fungi, and seven animals by bisulfite sequencing. The data suggest that land plants and vertebrates, which have extensive DNA methylation, are under strong selective pressure to repress TEs, because of their sexual mode of reproduction. Unicellular animals and fungi that reproduce asexually are more likely to lose TE methylation. Although gene body methylation is evolutionarily ancient, it is also mutagenic, and so loss of this pathway has been relatively common and occurred early in fungal evolution and later in several plant and animal lineages.


Eukaryotic cytosine methylation represses transcription but also occurs in the bodies of active genes, and the extent of methylation biology conservation is unclear. We quantified DNA methylation in 17 eukaryotic genomes and found 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 that exclusion of histone H2A.Z from methylated DNA is conserved between plants and animals, and we present evidence for RNA-directed DNA methylation of fungal genes. 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.

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