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Cited by 239Epigenetics and DNA MethylationPlant Molecular Biology ResearchChromosomal and Genetic Variations

DNA methylation dynamics during early plant life

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Bouyer, Daniel, Kramdi, Amira, Kassam, Mohamed, Heese, Maren, Schnittger, Arp, Roudier, François, Colot, Vincent·2017·Genome Biology
DOI 10.1186/s13059-017-1313-0PMC PMC5611644
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Abstract

BACKGROUND: Cytosine methylation is crucial for gene regulation and silencing of transposable elements in mammals and plants. While this epigenetic mark is extensively reprogrammed in the germline and early embryos of mammals, the extent to which DNA methylation is reset between generations in plants remains largely unknown. RESULTS: Using Arabidopsis as a model, we uncovered distinct DNA methylation dynamics over transposable element sequences during the early stages of plant development. Specifically, transposable elements and their relics show invariably high methylation at CG sites but increasing methylation at CHG and CHH sites. This non-CG methylation culminates in mature embryos, where it reaches saturation for a large fraction of methylated CHH sites, compared to the typical 10-20% methylation level observed in seedlings or adult plants. Moreover, the increase in CHH methylation during embryogenesis matches the hypomethylated state in the early endosperm. Finally, we show that interfering with the embryo-to-seedling transition results in the persistence of high CHH methylation levels after germination, specifically over sequences that are targeted by the RNA-directed DNA methylation (RdDM) machinery. CONCLUSION: Our findings indicate the absence of extensive resetting of DNA methylation patterns during early plant life and point instead to an important role of RdDM in reinforcing DNA methylation of transposable element sequences in every cell of the mature embryo. Furthermore, we provide evidence that this elevated RdDM activity is a specific property of embryogenesis.

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  • DNA methylation in plants can have significant impacts on gene regulation and in turn impact the overall plant uptake physiology.

    “DNA methylation in plants can have significant impacts on gene regulation and in turn impact the overall plant uptake physiology [29].”

    From Enhanced tolerance of industrial hemp (Cannabis sativa L.) plants on abandoned mine land soil leads to overexpression of cannabinoids (2019) · cites this paper as [29]

    The Background states that DNA methylation regulates specific genes in plants, supporting the gene-regulation part of the claim. Our copy does not link that regulation to plant uptake physiology; searches for uptake, nutrient transport, and physiology found no such passage. The indexed passages provide section labels but no page numbers. (LLM, conf=0.86)

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Authors
Bouyer, D., Kramdi, A., Kassam, M., Heese, M., Schnittger, A., Roudier, F., & Colot, V.
Affiliations
  • Centre National de la Recherche Scientifique (FR)
  • Lyon 1 Université (FR)
Corresponding author
Bouyer, Daniel
ORCID
Venue
Genome Biology
Publisher
Springer Science and Business Media LLC
Published
2017-09-25
Volume
18
Issue
1
Pages
179-179
ISSN
  • 1465-6906 (ISSN-L)
  • 1474-760X
DOI
10.1186/s13059-017-1313-0
PMC
PMC5611644
OpenAlex
W2756351847
Cited by
239
References
0
Citations by year
2026: 18 · 2025: 16 · 2024: 34 · 2023: 23 · 2022: 28 · 2021: 32 · 2020: 30 · 2019: 31 · 2018: 24 · 2017: 2
FWCI
9.72
Type
journal article
Language
en
Open access
Licence
cc-by
Locations
  • Genome biology (publishedVersion, cc-by)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • HAL (submittedVersion)
  • HAL (submittedVersion, other-oa)
  • HAL (submittedVersion, cc-by)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders
  • Agence Nationale de la Recherche (ANR-12-ADAP-0020-01, ANR-14-CE19-0008)
  • Cordis (HEALTH-F4-2010-257082)
  • European Research Council (210867-2)
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 › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
Keywords
DNA methylation dynamics, transposable elements, Arabidopsis thaliana, embryonic development, CHH methylation, CHG methylation, CG methylation, RNA-directed DNA methylation, epigenetic reprogramming, transposon silencing
MeSH terms
DNA Transposable Elements, Arabidopsis, Gene Expression Regulation, Plant, Gene Expression Regulation, Developmental, Genome, Plant, CpG Islands, DNA Methylation

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