title: Conservation and divergence of methylation patterning in plants and animals.
abstract: Cytosine DNA methylation is a heritable epigenetic mark present in many eukaryotic organisms. Although DNA methylation likely has a conserved role in gene silencing, the levels and patterns of DNA methylation appear to vary drastically among different organisms. Here we used shotgun genomic bisulfite sequencing (BS-Seq) to compare DNA methylation in eight diverse plant and animal genomes. We found that patterns of methylation are very similar in flowering plants with methylated cytosines detected in all sequence contexts, whereas CG methylation predominates in animals. Vertebrates have methylation throughout the genome except for CpG islands. Gene body methylation is conserved with clear preference for exons in most organisms. Furthermore, genes appear to be the major target of methylation in Ciona and honey bee. Among the eight organisms, the green alga Chlamydomonas has the most unusual pattern of methylation, having non-CG methylation enriched in exons of genes rather than in repeats and transposons. In addition, the Dnmt1 cofactor Uhrf1 has a conserved function in maintaining CG methylation in both transposons and gene bodies in the mouse, Arabidopsis, and zebrafish genomes.
authors.affiliation: Howard Hughes Medical Institute, Department of Molecular, Cell and Developmental Biology, and Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095, USA.
authors.forename: Suhua
authors.initials: S
authors.lastname: Feng
authors.forename: Shawn J
authors.initials: SJ
authors.lastname: Cokus
authors.forename: Xiaoyu
authors.initials: X
authors.lastname: Zhang
authors.forename: Pao-Yang
authors.initials: PY
authors.lastname: Chen
authors.forename: Magnolia
authors.initials: M
authors.lastname: Bostick
authors.forename: Mary G
authors.initials: MG
authors.lastname: Goll
authors.forename: Jonathan
authors.initials: J
authors.lastname: Hetzel
authors.forename: Jayati
authors.initials: J
authors.lastname: Jain
authors.forename: Steven H
authors.initials: SH
authors.lastname: Strauss
authors.forename: Marnie E
authors.initials: ME
authors.lastname: Halpern
authors.forename: Chinweike
authors.initials: C
authors.lastname: Ukomadu
authors.forename: Kirsten C
authors.initials: KC
authors.lastname: Sadler
authors.forename: Sriharsa
authors.initials: S
authors.lastname: Pradhan
authors.forename: Matteo
authors.initials: M
authors.lastname: Pellegrini
authors.forename: Steven E
authors.initials: SE
authors.lastname: Jacobsen
mesh_terms: D000818:Animals; D017360:Arabidopsis / Q000235:genetics; D019175:DNA Methylation / Q000235:genetics*; D019143:Evolution, Molecular; D005091:Exons / Q000235:genetics; D007438:Introns / Q000235:genetics; D009154:Mutation / Q000235:genetics; D020411:Oligonucleotide Array Sequence Analysis; D016366:Open Reading Frames / Q000235:genetics; D010802:Phylogeny; D010944:Plants / Q000235:genetics*; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics; D015534:Trans-Activators / Q000235:genetics; D015027:Zebrafish / Q000235:genetics; D029961:Zebrafish Proteins / Q000235:genetics
chemical_list: D015534:Trans-Activators; C517793:Uhrf1 protein, zebrafish; D029961:Zebrafish Proteins
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