DATE2025.12.04 #Press Releases

Plants’ Unique Mechanism for Gradually Silencing Unused Genes

-A Model in Which H3K4me2 Drives Stepwise Chromatin Repression in Plants through H3K4me2-Mediated Hierarchical Suppression of Chromatin-

Summary

A research team led by Takumi Noyori (graduate student, University of Tokyo) and Shusei Mori (then Project Researcher), together with Satoyo Oya (then Project Assistant Professor), Associate Professor Soichi Inagaki, and Professor Emeritus Tetsuji Kakutani (then Professor), in collaboration with Professor Hiroshi Kudoh of the Ecology Research Center at Kyoto University and Lecturer Haruki Nishio of the AI & Data Science Innovation Center at Shiga University, has revealed that histone H3 lysine 4 dimethylation (H3K4me2)—previously regarded as a marker of transcriptional activation—plays a critical role in regulating transcriptionally repressed states in plants.

Through genetic analyses and time-course experiments using the model plant Arabidopsis thaliana, the study shows that the accumulation of H3K4me2 within gene bodies facilitates the enrichment of repressive histone variants and modifications, including H2A.Z, H2A ubiquitination (H2Aub), and H3 lysine 27 trimethylation (H3K27me3). These marks promote the transition of chromatin into a repressed state, establishing a multilayered mechanism of chromatin repression unique to plants.

Although H3K4me2 has long been implicated in key developmental processes—such as shoot regeneration from undifferentiated cells and the regulation of flowering time—its precise molecular functions have remained unclear. This study substantially advances our understanding of the epigenetic mechanisms that underlie plant-specific development and environmental responses.

Figure：A model in which H3K4me2 mediates stepwise chromatin repression in plants

Journals

Journal name	Nature Communications
Title of paper	H3K4me2 orchestrates H2A.Z and Polycomb repressive marks in Arabidopsis