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PreprintCited by 1Plant Molecular Biology ResearchEpigenetics and DNA MethylationGenomics and Chromatin Dynamics

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H3K4me1 directs H3K36me2 and H3K36me3 deposition in land plants

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Wu, Jiabing, Wang, Jiachen, Du, Kangxi, Li, Yingping, Xie, Wenhao, He, Chenxi, Xing, Qidan, Li, Xiang, Zhu, Xiaoyu, Wu, Zhen, Wu, Xiaolong, Shen, Wen-Hui, Lan, Fei, Gan, Jianhua, Liu, Bing, Dong, Aiwu·2025·Nature Communications
DOI 10.1101/2025.06.06.658275PMC PMC13022364

Preprint — published as 10.1038/s41467-026-69632-5

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Abstract

Monomethylation of histone H3 lysine 4 (H3K4me1) marks enhancers in mammals. However, the function of H3K4me1 in plants remains largely unclear. Here, we analyzed the genome-wide distribution of H3K4me1 in diverse species across evolution, revealing a distinctive H3K4me1 distribution pattern in land plants. To explore the function of H3K4me1 in plants, we identified an H3K4me1-specific reader protein, Early heading date 3 (Ehd3), and solved the structure of Ehd3 in complex with the H3K4me1 peptide, revealing a unique binding module differing from the previously reported PHD finger proteins. We further identified an Ehd3-binding protein, SET domain group 724 (SDG724), and the deletion of either Ehd3 or SDG724 caused similar defects in plant phenotype and changes in transcriptome and epigenome profiles. Both Ehd3 and SDG724 are enriched at chromatin regions marked by H3K4me1 but not H3K4me2 or H3K4me3. Ehd3 activates the H3K36 methyltransferase SDG724, and H3K36me2/me3 are colocalized with H3K4me1 in the genomes of land plants. Collectively, our results reveal that H3K4me1 directs the establishment of H3K36me2 and H3K36me3 in land plants.

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Metadata

Authors
Wu, J., Wang, J., Du, K., Li, Y., Xie, W., He, C., Xing, Q., Li, X., Zhu, X., Wu, Z., Wu, X., Shen, W.-H., Lan, F., Gan, J., Liu, B., & Dong, A.
Affiliations
  • Shaoxing University (CN)
  • Fudan University (CN)
  • Centre National de la Recherche Scientifique (FR)
Corresponding author
  • Gan, Jianhua
  • Liu, Bing
  • Dong, Aiwu
ORCID
Venue
Nature Communications
Publisher
openRxiv
Published
2025-06-07
Volume
17
Issue
1
ISSN
2041-1723 (ISSN-L)
DOI
10.1101/2025.06.06.658275
PMC
PMC13022364
OpenAlex
W7129105332
Cited by
1
References
94
Citations by year
2026: 1
FWCI
3.70
Type
journal article
Language
en
Open access
Licence
Locations
  • Nature Communications (publishedVersion, cc-by-nc-nd)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
  • PubMed Central (publishedVersion, cc-by-nc-nd)
  • PubMed (publishedVersion)
  • HAL (submittedVersion, other-oa)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders
  • National Key Research and Development Program of China (2024YFE0105100)
  • the Open Research Fund of State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University (SKL-KF202412)
Topics
  • Life Sciences › Agricultural and Biological Sciences › Plant Science › Plant Molecular Biology Research
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
Keywords
H3K4me1, H3K36me2, H3K36me3, histone methylation, land plants, EHD3, histone reader proteins, PHD finger, chromatin regulation, enhancer function, epigenome
MeSH terms
Chromatin, Histones, Lysine, Methylation, Plant Proteins, Arabidopsis, Gene Expression Regulation, Plant, Embryophyta

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