Conservation and divergence of methylation patterning in plants and animals
Open accessAbstract
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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The establishment, maintenance, and removal of epigenetic marks are critical during neurodevelopment, and when disrupted can have significant impacts on neurodevelopment and cognitive function.
“The establishment, maintenance, and removal of epigenetic marks are critical during neurodevelopment and when disrupted can have significant impacts on neurodevelopment and cognitive function [ 63–66 ].”
From DNA methylation: a mechanism linking environmental chemical exposures to risk of autism spectrum disorders? (2016) · cites this paper as [64]
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- Authors
- Feng, S., Cokus, S. J., Zhang, X., Chen, P.-Y., Bostick, M., Goll, M. G., Hetzel, J., Jain, J., Strauss, S. H., Halpern, M. E., Ukomadu, C., Sadler, K. C., Pradhan, S., Pellegrini, M., & Jacobsen, S. E.
- Affiliations
- Howard Hughes Medical Institute (US)
- University of California, Los Angeles (US)
- University of Georgia (US)
- Department of Molecular, Cell and Developmental Biology, and
- Carnegie Institution for Science (US)
- Oregon State University (US)
- Brigham and Women's Hospital (US)
- Icahn School of Medicine at Mount Sinai (US)
- New England Biolabs (United States) (US)
- ORCID
- Venue
- Proceedings of the National Academy of Sciences
- Publisher
- National Academy of Sciences
- Published
- 2010-04-15
- Volume
- 107
- Issue
- 19
- Pages
- 8689-8694
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- PMC
- PMC2889301
- OpenAlex
- W2149206894
- Cited by
- 1,285
- References
- 40
- Citations by year
- 2026: 45 · 2025: 61 · 2024: 60 · 2023: 60 · 2022: 96 · 2021: 105 · 2020: 86 · 2019: 77 · 2018: 76 · 2017: 96 · 2016: 86 · 2015: 94 · 2014: 89 · 2013: 84 · 2012: 71
- FWCI
- 32.98
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Proceedings of the National Academy of Sciences (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- Howard Hughes Medical Institute
- National Institutes of Health (1f32ca126302-01)
- National Cancer Institute (5F32CA126302, F32 CA126302)
- National Institute of General Medical Sciences (GM60398, R37GM060398, R01GM060398)
- National Institute of Diabetes and Digestive and Kidney Diseases (R01DK080789)
- Eunice Kennedy Shriver National Institute of Child Health and Human Development (R01HD058530)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Syndromes and Imprinting
- Keywords
- DNA methylation, cytosine methylation, epigenetic inheritance, gene silencing, CG methylation, non-CG methylation, gene body methylation, CpG islands, UHRF1, Chlamydomonas, Ciona, Apis mellifera, comparative epigenomics, flowering plants, vertebrates
- MeSH terms
- Animals, Exons, Introns, Mutation, Phylogeny, Plants, Repetitive Sequences, Nucleic Acid, Zebrafish, Trans-Activators, Open Reading Frames, Arabidopsis, Evolution, Molecular, DNA Methylation, Oligonucleotide Array Sequence Analysis, Zebrafish Proteins
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