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

Research output: Contribution to journalArticlepeer-review

2 Scopus citations


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.

Original languageEnglish
Article number106
JournalGenome Biology
Issue number1
StatePublished - Dec 2023

Bibliographical note

Funding Information:
This work was supported by grants from the Next-Generation BioGreen 21 Program (PJ013423) funded by the Rural Development Administration, the National Research Foundation of Korea (NRF) grant funded by the Korea government (MSIT) (2020R1A2C3012750). SL was supported by the Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education (2019R1I1A1A01055449). A fellowship from the Human Frontier Science Program (LT000667/2013) to JC.

Publisher Copyright:
© 2023, The Author(s).


  • Chromatin remodeler DDM1
  • Gene body methylation
  • Natural epigenetic variation
  • Priming


Dive into the research topics of 'DDM1-mediated gene body DNA methylation is associated with inducible activation of defense-related genes in Arabidopsis'. Together they form a unique fingerprint.

Cite this