Epigenetic gene regulation in plants and its potential applications in crop improvement

doi:10.1038/s41580-024-00769-1

Review

. 2025 Jan;26(1):51-67.

doi: 10.1038/s41580-024-00769-1. Epub 2024 Aug 27.

Epigenetic gene regulation in plants and its potential applications in crop improvement

Heng Zhang¹, Jian-Kang Zhu²

Affiliations

¹ Department of Genetics and Developmental Science, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China. zhangheng82@sjtu.edu.cn.
² Institute of Advanced Biotechnology and School of Medicine, Southern University of Science and Technology, Shenzhen, China. zhujk@sustech.edu.cn.

PMID: 39192154
DOI: 10.1038/s41580-024-00769-1

Review

Epigenetic gene regulation in plants and its potential applications in crop improvement

Heng Zhang et al. Nat Rev Mol Cell Biol. 2025 Jan.

. 2025 Jan;26(1):51-67.

doi: 10.1038/s41580-024-00769-1. Epub 2024 Aug 27.

Authors

Heng Zhang¹, Jian-Kang Zhu²

Affiliations

¹ Department of Genetics and Developmental Science, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China. zhangheng82@sjtu.edu.cn.
² Institute of Advanced Biotechnology and School of Medicine, Southern University of Science and Technology, Shenzhen, China. zhujk@sustech.edu.cn.

PMID: 39192154
DOI: 10.1038/s41580-024-00769-1

Abstract

DNA methylation, also known as 5-methylcytosine, is an epigenetic modification that has crucial functions in plant growth, development and adaptation. The cellular DNA methylation level is tightly regulated by the combined action of DNA methyltransferases and demethylases. Protein complexes involved in the targeting and interpretation of DNA methylation have been identified, revealing intriguing roles of methyl-DNA binding proteins and molecular chaperones. Structural studies and in vitro reconstituted enzymatic systems have provided mechanistic insights into RNA-directed DNA methylation, the main pathway catalysing de novo methylation in plants. A better understanding of the regulatory mechanisms will enable locus-specific manipulation of the DNA methylation status. CRISPR-dCas9-based epigenome editing tools are being developed for this goal. Given that DNA methylation patterns can be stably transmitted through meiosis, and that large phenotypic variations can be contributed by epimutations, epigenome editing holds great promise in crop breeding by creating additional phenotypic variability on the same genetic material.

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Conflict of interest statement

Competing interests: The authors declare no competing interests.

References

1. Li, E., Bestor, T. H. & Jaenisch, R. Targeted mutation of the DNA methyltransferase gene results in embryonic lethality. Cell 69, 915–926 (1992). - PubMed - DOI
1. Okano, M., Bell, D. W., Haber, D. A. & Li, E. DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development. Cell 99, 247–257 (1999). - PubMed - DOI
1. Alleman, M. et al. An RNA-dependent RNA polymerase is required for paramutation in maize. Nature 442, 295–298 (2006). - PubMed - DOI
1. He, L. et al. DNA methylation-free Arabidopsis reveals crucial roles of DNA methylation in regulating gene expression and development. Nat. Commun. 13, 1335 (2022). - PubMed - PMC - DOI
1. Schmitz, R. J., Lewis, Z. A. & Goll, M. G. DNA methylation: shared and divergent features across eukaryotes. Trends Genet. 35, 818–827 (2019). - PubMed - PMC - DOI

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[1] Li, E., Bestor, T. H. & Jaenisch, R. Targeted mutation of the DNA methyltransferase gene results in embryonic lethality. Cell 69, 915–926 (1992). - PubMed - DOI

[2] Li, E., Bestor, T. H. & Jaenisch, R. Targeted mutation of the DNA methyltransferase gene results in embryonic lethality. Cell 69, 915–926 (1992). - PubMed - DOI

[3] Okano, M., Bell, D. W., Haber, D. A. & Li, E. DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development. Cell 99, 247–257 (1999). - PubMed - DOI

[4] Okano, M., Bell, D. W., Haber, D. A. & Li, E. DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development. Cell 99, 247–257 (1999). - PubMed - DOI

[5] Alleman, M. et al. An RNA-dependent RNA polymerase is required for paramutation in maize. Nature 442, 295–298 (2006). - PubMed - DOI

[6] Alleman, M. et al. An RNA-dependent RNA polymerase is required for paramutation in maize. Nature 442, 295–298 (2006). - PubMed - DOI

[7] He, L. et al. DNA methylation-free Arabidopsis reveals crucial roles of DNA methylation in regulating gene expression and development. Nat. Commun. 13, 1335 (2022). - PubMed - PMC - DOI

[8] He, L. et al. DNA methylation-free Arabidopsis reveals crucial roles of DNA methylation in regulating gene expression and development. Nat. Commun. 13, 1335 (2022). - PubMed - PMC - DOI

[9] Schmitz, R. J., Lewis, Z. A. & Goll, M. G. DNA methylation: shared and divergent features across eukaryotes. Trends Genet. 35, 818–827 (2019). - PubMed - PMC - DOI

[10] Schmitz, R. J., Lewis, Z. A. & Goll, M. G. DNA methylation: shared and divergent features across eukaryotes. Trends Genet. 35, 818–827 (2019). - PubMed - PMC - DOI

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Epigenetic gene regulation in plants and its potential applications in crop improvement

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Epigenetic gene regulation in plants and its potential applications in crop improvement

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