A Key Factor in Soybean Epigenetics — Soybean DDM1 Regulates Both Transposons and Genes —

June 04, 2026

Key points

  • The absence of DDM1 results in post-germination lethality in soybeans.
  • DDM1 is required for the expression of photosynthetic genes in edamame (immature seed stage of soybean seeds).
  • The effects of a partial decrease in DDM1 primarily manifest as the derepression of genes in euchromatin regions.

The nuclear genome of eukaryotes, including flowering plants, is divided into two regions: euchromatin1, which has high density of genes, and heterochromatin, which has many repetitive sequences, such as transposons (mobile DNA sequences)2. In plants, heterochromatin is epigenetically3 suppressed through mechanisms such as DNA methylation, and the chromatin remodeling factor Decreased in DNA methylation 1 (DDM1)4 plays a central role in this process. A research group led by Ahsen Gers, a doctoral student in the Graduate School of Natural Science and Technology at Niigata University; Associate Professor Kaoru Tonosaki of Yokohama City University; Dr. Akito Kaga of the National Agriculture and Food Research Organization (NARO); Project Professor Atsushi Toyoda of the National Institute of Genetics; Division Director Taiji Kawakatsu of the RIKEN BioResource Research Center; and Associate Professor Eigo Fukai of the Faculty of Agriculture at Niigata University has revealed that in soybeans, DDM1 is also involved in the regulation of gene expression in euchromatin.

[Term explanations]

1. Euchromatin and Heterochromatin
Chromatin is a complex of DNA and proteins such as histones. In the nuclear genome, regions where chromatin is tightly packed and condensed are called heterochromatin, whereas regions where chromatin is loosely condensed and open are called euchromatin. In the heterochromatin, transcription from DNA to RNA tend to be suppressed, whereas in the euchromatin, it tends to be active.

2. Transposon (mobile DNA)
DNA sequences capable of moving within a genome is called transposons. Transposon is an endogenous mutagen.

3. Epigenetics
A general term for heritable information other than DNA sequence. For example, cytosine in the nuclear genomic DNA of eukaryotes can be modified by adding a methyl groups, a process called DNA methylation. DNA methylation can alter transcription efficiency from DNA to RNA.

4. Decreased in DNA methylation 1 (DDM1)
A chromatin-remodeling factor essential for maintaining heterochromatin in plants. The mammalian ortholog of DDM1 is HELLS/LSH. This heterochromatin regulatory system is believed to be widely conserved in eukaryotes.

Publication Details

Journal:The Plant Journal
Title:Differential regulation of heterochromatin and euchromatin by GmDDM1 during seed development ensures seedling viability in soybean.
Authors:Ahsen Gers, Kana Shiraishi, Kaoru Tonosaki, Satoru Okamoto, Akito Kaga, Ryota Kuroda, Jun-Ichi Matsuoka, Atsushi Toyoda, Taiji Kawakatsu, Chiho Maruko, Kazuki Takahashi, Keiichi Okazaki, Moeko Okada and Eigo Fukai
Doi: 10.1111/tpj.70921

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