Whole-Genome Analysis of Histone H3 Lysine 27 Trimethylation in Arabidopsis
Open accessAbstract
Trimethylation of histone H3 lysine 27 (H3K27me3) plays critical roles in regulating animal development, and in several cases, H3K27me3 is also required for the proper expression of developmentally important genes in plants. However, the extent to which H3K27me3 regulates plant genes on a genome-wide scale remains unknown. In addition, it is not clear whether the establishment and spreading of H3K27me3 occur through the same mechanisms in plants and animals. We identified regions containing H3K27me3 in the genome of the flowering plant Arabidopsis thaliana using a high-density whole-genome tiling microarray. The results suggest that H3K27me3 is a major silencing mechanism in plants that regulates an unexpectedly large number of genes in Arabidopsis (~4,400), and that the maintenance of H3K27me3 is largely independent of other epigenetic pathways, such as DNA methylation or RNA interference. Unlike in animals, where H3K27m3 occupies large genomic regions, in Arabidopsis, we found that H3K27m3 domains were largely restricted to the transcribed regions of single genes. Furthermore, unlike in animals systems, H3K27m3 domains were not preferentially associated with low-nucleosome density regions. The results suggest that different mechanisms may underlie the establishment and spreading of H3K27me3 in plants and animals.
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Zhang et al. identified that H3K27me3 regulates approximately 4400 genes in Arabidopsis, independent of small RNAs or DNA methylation pathways.
“Zhang et al. highlighted the widespread silencing role of H3K27me3, identifying its regulation of approximately 4400 genes in Arabidopsis, independent of small RNAs or DNA methylation pathways [58].”
From Somaclonal Variation and Clonal Fidelity in Commercial Micropropagation: Challenges and Perspectives (2025) · cites this paper as [58]
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“similar to that observed in animals and fungi [31,37–41], Figure 4.”
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Bernatavichute, Y. V., Zhang, X., Cokus, S., Pellegrini, M., & Jacobsen, S. E. (2008) · PLoS ONE · doi:10.1371/journal.pone.0003156 · Cited by 333 · see citing works
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Somaclonal Variation and Clonal Fidelity in Commercial Micropropagation: Challenges and Perspectives
Majumder, S., Igamberdiev, A. U., & Debnath, S. C. (2025) · Agronomy · doi:10.3390/agronomy15061489 · Cited by 46 · see citing works
- Authors
- Zhang, X., Clarenz, O., Cokus, S., Bernatavichute, Y. V., Pellegrini, M., Goodrich, J., & Jacobsen, S. E.
- Affiliations
- University of California, Los Angeles (US)
- University of Edinburgh (GB)
- Howard Hughes Medical Institute (US)
- Corresponding author
- Jacobsen, Steven E
- Venue
- PLoS Biology
- Publisher
- Public Library of Science (PLoS)
- Published
- 2007-04-17
- Volume
- 5
- Issue
- 5
- Pages
- e129
- ISSN
- 1544-9173 (ISSN-L)
- 1545-7885
- PMC
- PMC1852588
- OpenAlex
- W2025040226
- Cited by
- 767
- References
- 1
- Citations by year
- 2026: 19 · 2025: 31 · 2024: 32 · 2023: 31 · 2022: 43 · 2021: 53 · 2020: 33 · 2019: 41 · 2018: 24 · 2017: 36 · 2016: 43 · 2015: 41 · 2014: 37 · 2013: 49 · 2012: 42
- FWCI
- 20.15
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- PLoS Biology (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- eScholarship (California Digital Library) (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion, cc-by)
- Figshare (submittedVersion, cc-by)
- Edinburgh Research Explorer (University of Edinburgh) (submittedVersion, cc-by)
- Funders
- Howard Hughes Medical Institute
- Deutsche Forschungsgemeinschaft
- National Institutes of Health (GM60398, grant GM60398)
- U.S. Public Health Service (GM07104)
- Biotechnology and Biological Sciences Research Council (G20266)
- National Human Genome Research Institute (R01HG003523, HG003523)
- National Institute of General Medical Sciences (T32GM007104, GM60398, R37GM060398, R01GM060398, GM 07104)
- Jonsson Cancer Center Foundation
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Plant Molecular Biology Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Keywords
- H3K27me3, Arabidopsis thaliana, epigenetic silencing, gene silencing, chromatin domains, epigenetic inheritance, DNA methylation, RNA interference, nucleosome density, plant development
- MeSH terms
- Amino Acid Sequence, Histones, Lysine, Methylation, Histone-Lysine N-Methyltransferase, Genes, Plant, Arabidopsis, Genome, Plant, Gene Silencing
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