Review Article | Published:

Dynamics and function of DNA methylation in plants

Nature Reviews Molecular Cell Biologyvolume 19pages489506 (2018) | Download Citation

Abstract

DNA methylation is a conserved epigenetic modification that is important for gene regulation and genome stability. Aberrant patterns of DNA methylation can lead to plant developmental abnormalities. A specific DNA methylation state is an outcome of dynamic regulation by de novo methylation, maintenance of methylation and active demethylation, which are catalysed by various enzymes that are targeted by distinct regulatory pathways. In this Review, we discuss DNA methylation in plants, including methylating and demethylating enzymes and regulatory factors, and the coordination of methylation and demethylation activities by a so-called methylstat mechanism; the functions of DNA methylation in regulating transposon silencing, gene expression and chromosome interactions; the roles of DNA methylation in plant development; and the involvement of DNA methylation in plant responses to biotic and abiotic stress conditions.

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Acknowledgements

The authors apologize to those colleagues whose work is not cited owing to space constraints. The work of the authors has been supported by the Chinese Academy of Sciences.

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Nature Reviews Molecular Cell Biology thanks F. Berger, V. Colot and X. Zhong for their contribution to the peer review of this work.

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Affiliations

  1. Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences, Shanghai, China

    • Huiming Zhang
    • , Zhaobo Lang
    •  & Jian-Kang Zhu
  2. CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China

    • Huiming Zhang
    • , Zhaobo Lang
    •  & Jian-Kang Zhu
  3. Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, USA

    • Jian-Kang Zhu

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Contributions

H.Z. and J.-K.Z. researched data for the article, provided substantial contributions to the discussion of content and wrote the article. H.Z., Z.L. and J.-K.Z. reviewed and edited the manuscript before submission.

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The authors declare no competing interests.

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Correspondence to Huiming Zhang or Jian-Kang Zhu.

Supplementary information

Glossary

AGO hook

A protein motif containing Gly–Trp or Try–Gly repeats, which mediate protein interactions with ARGONAUTE (AGO) proteins.

Ribosomal RNA-processing 6

(RRP6). A conserved single-stranded RNA nuclease with both negative and positive functions in RNA accumulation.

Trans-acting siRNA genes

Genes that encode transcripts that are cleaved by microRNAs, synthesized into double-stranded RNA and then cleaved again to produce trans-acting small interfering RNAs (siRNAs).

α-Crystallin domain

A motif of approximately 100 amino acids that is characteristic of evolutionarily conserved small heat shock proteins.

Helitron

A major class of eukaryotic transposons that transpose through rolling-circle replication.

Homeotic gene

A gene that controls pattern formation during development.

Mantled

A type of abnormality in oil palm male floral organs in which they transform into supernumerary carpels.

Columella cells

A layer of cells that form the root cap and protect the growing root tip.

Allotetraploid

A polyploid with four sets of chromosomes derived from two or more diverged taxa.

Heterosis

The increase in characteristics, such as size and yield, of a hybrid organism over those of its parents.

Nucleotide-binding and oligomerization domain-like receptors

Receptors that mediate recognition of pathogen avirulence effectors and activate immune responses.

Biotrophic pathogen

A pathogen that feeds on only live host cells.

Necrotrophic pathogens

Pathogens that feed on nutrients released from dead cells.

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https://doi.org/10.1038/s41580-018-0016-z