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Annual Review of Plant Biology

Volume 76, 2025

Molecular Mechanisms Underlying the Establishment, Maintenance, and Removal of DNA Methylation in Plants

  • Guohui Xie1,*, Xuan Du2,*, Hongmiao Hu3,* and Jiamu Du1,4
  • 1Shenzhen Key Laboratory of Plant Genetic Engineering and Molecular Design, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China; email: [email protected] 2Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China 3MRC Laboratory of Molecular Biology, Cambridge, United Kingdom 4Institute for Biological Electron Microscopy, Southern University of Science and Technology, Shenzhen, China
    * These authors contributed equally to this article
  • Vol. 76:143-170 (Volume publication date May 2025)
  • First published as a Review in Advance on March 03, 2025
  • Copyright © 2025 by the author(s).
    This work is licensed under a Creative Commons Attribution 4.0 International License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. See credit lines of images or other third-party material in this article for license information.

Abstract

Methylation at the fifth position of the cytosine base (5mC) is a critical DNA modification with important functions in gene silencing, genome imprinting, and suppression of transposable elements in eukaryotes. Biochemically, DNA methylation is dynamically regulated by three critical processes: the de novo establishment of DNA methylation, the maintenance of DNA methylation by preexisting methylation patterns, and the removal of DNA methylation. In plants, DNA methylation is very complex with unique features. In past decades, a series of biochemical and structural studies, especially empowered by the recent breakthroughs of high-resolution cryogenic electron microscopy, have helped uncover the molecular mechanisms underlying the establishment, maintenance, and removal of DNA methylation in plants. This review summarizes recent research advances in these three aspects of DNA methylation and lays out a molecular view of plant DNA methylation from biochemical and structural perspectives.

Keyword(s): DNA demethylation, epigenetic regulation, histone modification, long noncoding RNA, RNA-directed DNA methylation, small interfering RNA
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2025-05-20
2025-06-20
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/content/journals/10.1146/annurev-arplant-083123-054357
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Molecular Mechanisms Underlying the Establishment, Maintenance, and Removal of DNA Methylation in Plants
Annual Review of Plant Biology 76, 143 (2025); https://doi.org/10.1146/annurev-arplant-083123-054357
/content/journals/10.1146/annurev-arplant-083123-054357
/content/journals/10.1146/annurev-arplant-083123-054357
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