Conservation and divergence of methylation patterning in plants and animals

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 bisulfit...

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Published inProceedings of the National Academy of Sciences - PNAS Vol. 107; no. 19; pp. 8689 - 8694
Main Authors Feng, Suhua, Cokus, Shawn J, Zhang, Xiaoyu, Chen, Pao-Yang, Bostick, Magnolia, Goll, Mary G, Hetzel, Jonathan, Jain, Jayati, Strauss, Steven H, Halpern, Marnie E, Ukomadu, Chinweike, Sadler, Kirsten C, Pradhan, Sriharsa, Pellegrini, Matteo, Jacobsen, Steven E
Format Journal Article
LanguageEnglish
Published United States National Academy of Sciences 11.05.2010
National Acad Sciences
SeriesFrom the Cover
Subjects
animal genetics
Animals
Apis mellifera
Aquatic plants
Arabidopsis
Arabidopsis - genetics
Biological Sciences
Chlamydomonas
Ciona
Comparative analysis
cytosine
Danio rerio
Deoxyribonucleic acid
DNA
DNA methylation
DNA Methylation - genetics
DNA methylation patterns
Eukaryotes
Evolution, Molecular
Exons
Exons - genetics
Flowering plants
Flowers & plants
gene body methylation
Genes
Genomes
Genomics
Honey bees
insect genetics
Insect genomes
insects
interspecific variation
Introns
Introns - genetics
methyl bromide
Methylation
Mutation - genetics
Oligonucleotide Array Sequence Analysis
Open Reading Frames - genetics
Phylogeny
plant genetics
Plants
Plants - genetics
repetitive sequences
Repetitive Sequences, Nucleic Acid - genetics
sequence analysis
shotgun genomic bisulfite sequencing
species differences
Trans-Activators - genetics
Transposons
Vertebrates
Zebrafish - genetics
Zebrafish Proteins - genetics
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Summary: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.
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Author contributions: S.H.S., M.E.H., C.U., K.C.S., S.P., M.P., and S.E.J. designed research; S.F., M.B., M.G.G., J.H., and J.J. performed research; S.F., S.J.C., X.Z., P.-Y.C., M.P., and S.E.J. analyzed data; and S.F., S.J.C., M.P., and S.E.J. wrote the paper.
Edited* by James C. Carrington, Oregon State University, Corvallis, OR, and approved March 19, 2010 (received for review March 4, 2010)
1S.F. and S.J.C. contributed equally to this work.
ISSN:0027-8424
1091-6490
1091-6490
DOI:10.1073/pnas.1002720107