Regulation of plant immunity through histone H3 β-hydroxybutyrylation-mediated transcriptional control

Qiutao Xu, Zhengting Chen, Wang Rui, Xuan Ma, Yuhang Duan, Du Hai, Jing Chen, Zhongyi Cheng, Lu Zheng, Junbin Huang, Jisen Zhang, Yu Zhao () and Xiaoyang Chen ()
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Qiutao Xu: Guangxi University
Zhengting Chen: China National Rice Research Institute
Wang Rui: Yangtze University
Xuan Ma: Ningxia University
Yuhang Duan: Huazhong Agricultural University
Du Hai: Huazhong Agricultural University
Jing Chen: Anhui Agricultural University
Zhongyi Cheng: Jingjie PTM BioLab Co. Ltd
Lu Zheng: Huazhong Agricultural University
Junbin Huang: Huazhong Agricultural University
Jisen Zhang: Guangxi University
Yu Zhao: Huazhong Agricultural University
Xiaoyang Chen: Anhui Agricultural University

Nature Communications, 2025, vol. 16, issue 1, 1-17

Abstract: Abstract Histone lysine β-hydroxybutyrylation (Kbhb) is a novel type of histone acylation whose prevalence and function remain unclear in plants. Here, we systematically characterized H3K9bhb in rice (Oryza sativa) and found that it is enriched at transcription start site (TSS) regions and serves as an active mark for gene expression. We demonstrated functional differences between H3K9bhb and the well-studied H3K9ac histone modification, particularly in regulating genes involved in the rice immune response. We also discovered that the exogenous application of β-hydroxybutyrate induces H3K9bhb deposition and promotes the expression of defense-related genes, enhancing disease resistance. Furthermore, we identified OsSRT1, OsSRT2, and OsHDA705 as key players in the removal of Kbhb. We also conducted a Kbhb proteomic analysis and identified 2159 Kbhb sites on 1128 proteins, providing a valuable resource for future studies of Kbhb. This research advances our understanding of plant epigenetic regulation by establishing Kbhb as a cellular post-translational modification with the potential to regulate plant immune responses.

Date: 2025
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DOI: 10.1038/s41467-025-61474-x

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