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Genome-Wide Association of Histone H3 Lysine Nine Methylation with CHG DNA Methylation in Arabidopsis thaliana
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Methylation of histone H3 lysine 9 (H3K9) is a hallmark of transcriptional silencing in many organisms. In Arabidopsis thaliana, dimethylation of H3K9 (H3K9m2) is important in the silencing of transposons and in the control of DNA methylation. We constructed a high-resolution genome-wide map of H3K9m2 methylation by using chromatin immunoprecipitation coupled with whole genome Roche Nimblegen microarrays (ChIP-chip). We observed a very high coincidence between H3K9m2 and CHG methylation (where H is either A,T or C) throughout the genome. The coding regions of genes that are associated exclusively with methylation in a CG context did not contain H3K9m2. In addition, we observed two distinct patterns of H3K9m2. Transposons and other repeat elements present in the euchromatic arms contained small islands of H3K9m2 present at relatively low levels. In contrast, pericentromeric/centromeric regions of Arabidopsis chromosomes contained long, rarely interrupted blocks of H3K9m2 present at much higher average levels than seen in the chromosome arms. These results suggest a complex interplay between H3K9m2 and different types of DNA methylation and suggest that distinct mechanisms control H3K9m2 in different compartments of the genome.
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![Figure 1 Distribution of DNA methylation and K9H3m2 methylation along chromosomes. Top panels show average DNA methylation levels in a sliding 100 kb window [32]. Bottom panels show the number of H3K9m2 positive probes (z-score>0.2) in a sliding 100 kb window.](/paper-figures/49eb9e4a503940cdba3631fce0ed49c1/genome-wide-association-of-histone-h3-lysine-nine-methylation-with-chg-dna-figure-1.jpg)
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“For example, it is well known that modifications such as the ubiquitination of H2BK143, mono-, di-, and trimethylation of H3K4, H3K36, and H3 and H4 lysine acetylation are associated, in Arabidopsis genome, with gene activation, while the mono-, di- and trimethylation of H3H9, H3K27, and H4K20, and the dimethylation of H4R3, are associated with gene inactivation [90,91,92,93]).”
From Somaclonal Variation—Advantage or Disadvantage in Micropropagation of the Medicinal Plants (2023) · cites this paper as [92]
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Metadata
- Authors
- Bernatavichute, Y. V., Zhang, X., Cokus, S., Pellegrini, M., & Jacobsen, S. E.
- Affiliations
- University of California, Los Angeles (US)
- University of Georgia (US)
- Howard Hughes Medical Institute (US)
- Corresponding author
- Pellegrini, Matteo
- Jacobsen, Steven E.
- Venue
- PLoS ONE
- Publisher
- Public Library of Science (PLoS)
- Published
- 2008-09-08
- Volume
- 3
- Issue
- 9
- Pages
- e3156
- ISSN
- 1932-6203 (ISSN-L)
- PMC
- PMC2522283
- OpenAlex
- W1999644599
- Cited by
- 333
- References
- 55
- Citations by year
- 2026: 8 · 2025: 4 · 2024: 13 · 2023: 13 · 2022: 13 · 2021: 15 · 2020: 26 · 2019: 18 · 2018: 23 · 2017: 11 · 2016: 19 · 2015: 19 · 2014: 26 · 2013: 24 · 2012: 43
- FWCI
- 7.96
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- PLoS ONE (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion, cc-by)
- Figshare (submittedVersion, cc-by)
- Funders
- Howard Hughes Medical Institute
- National Institutes of Health (GM60398, grant GM60398)
- U.S. Public Health Service (GM07104)
- National Institute of General Medical Sciences (T32GM007104, GM60398, R37GM060398, R01GM060398)
- Jonsson Cancer Center Foundation
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Plant Molecular Biology Research
- Keywords
- H3K9 dimethylation, histone methylation, DNA methylation, transcriptional silencing, transposon silencing, centromeric heterochromatin, pericentromeric regions, CG methylation, repetitive elements, Arabidopsis thaliana, genome-wide methylation mapping
- MeSH terms
- Chromatin, DNA Transposable Elements, Heterochromatin, Histones, Lysine, Methylation, Transcription, Genetic, Genes, Plant, Arabidopsis, Genome, Plant, DNA Methylation, Arabidopsis Proteins, RNA, Small Interfering, Epigenesis, Genetic, Chromatin Immunoprecipitation, Genome-Wide Association Study
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