Genome-wide evolutionary analysis of eukaryotic DNA methylation.
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.
Zemach
Assaf
A
Department of Plant and Microbial Biology, 211 Koshland Hall, University of California, Berkeley, CA 94720, USA.
McDaniel
Ivy E
IE
Silva
Pedro
P
Zilberman
Daniel
D
D000818:Animals; D005075:Biological Evolution; D000460:Chlorophyta / Q000235:genetics; D018899:CpG Islands; D004248:DNA (Cytosine-5-)-Methyltransferases / Q000378:metabolism; D019175:DNA Methylation; D004251:DNA Transposable Elements; D056890:Eukaryota / Q000235:genetics* / Q000378:metabolism; D005658:Fungi / Q000235:genetics / Q000378:metabolism; D005786:Gene Expression Regulation; D016678:Genome; D016681:Genome, Fungal; D018745:Genome, Plant; D006657:Histones / Q000378:metabolism; D010802:Phylogeny; D010944:Plants / Q000235:genetics / Q000378:metabolism; D011401:Promoter Regions, Genetic; D012641:Selection, Genetic; D014158:Transcription, Genetic
D004251:DNA Transposable Elements; D006657:Histones; D004248:DNA (Cytosine-5-)-Methyltransferases