Genome Biology (May 2023)

DDM1-mediated gene body DNA methylation is associated with inducible activation of defense-related genes in Arabidopsis

  • Seungchul Lee,
  • Jaemyung Choi,
  • Jihwan Park,
  • Chang Pyo Hong,
  • Daeseok Choi,
  • Soeun Han,
  • Kyuha Choi,
  • Tae-Young Roh,
  • Daehee Hwang,
  • Ildoo Hwang

DOI
https://doi.org/10.1186/s13059-023-02952-7
Journal volume & issue
Vol. 24, no. 1
pp. 1 – 30

Abstract

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Abstract Background Plants memorize previous pathogen attacks and are “primed” to produce a faster and stronger defense response, which is critical for defense against pathogens. In plants, cytosines in transposons and gene bodies are reported to be frequently methylated. Demethylation of transposons can affect disease resistance by regulating the transcription of nearby genes during defense response, but the role of gene body methylation (GBM) in defense responses remains unclear. Results Here, we find that loss of the chromatin remodeler decrease in DNA methylation 1 (ddm1) synergistically enhances resistance to a biotrophic pathogen under mild chemical priming. DDM1 mediates gene body methylation at a subset of stress-responsive genes with distinct chromatin properties from conventional gene body methylated genes. Decreased gene body methylation in loss of ddm1 mutant is associated with hyperactivation of these gene body methylated genes. Knockout of glyoxysomal protein kinase 1 (gpk1), a hypomethylated gene in ddm1 loss-of-function mutant, impairs priming of defense response to pathogen infection in Arabidopsis. We also find that DDM1-mediated gene body methylation is prone to epigenetic variation among natural Arabidopsis populations, and GPK1 expression is hyperactivated in natural variants with demethylated GPK1. Conclusions Based on our collective results, we propose that DDM1-mediated GBM provides a possible regulatory axis for plants to modulate the inducibility of the immune response.

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