Evidence map›Paper›PMID 39934332›Full record

ArticleNature plants2025

Histone H3 lysine 4 methylation recruits DNA demethylases to enforce gene expression in Arabidopsis.

Ming Wang, Yan He, Zhenhui Zhong, Ashot Papikian, Shuya Wang, Jason Gardiner, Basudev Ghoshal, Suhua Feng, Yasaman Jami-Alahmadi, James A Wohlschlegel and 1 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nature plants, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.

0numbers the graph read from it
0cells of the map it votes in
16citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

16 citing papers in PubMed.

  1. Article
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  4. Review
  5. Genome-wide CG hypomethylation of theProceedings of the National Academy of Sciences of the United States of America · 2026
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  11. Review
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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

11 authors.

Ming Wang *State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.ORCID 0000-0002-1223-3421
Yan He *Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA, USA.
Zhenhui ZhongDepartment of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA, USA.ORCID 0000-0002-8438-0375
Ashot PapikianDepartment of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA, USA.ORCID 0000-0002-2801-6341
Shuya WangDepartment of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA, USA.
Jason GardinerDepartment of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA, USA.ORCID 0000-0001-9387-6383
Basudev GhoshalDepartment of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA, USA.ORCID 0000-0003-1387-0139
Suhua FengDepartment of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA, USA.
Yasaman Jami-AlahmadiDepartment of Biological Chemistry, University of California Los Angeles, Los Angeles, CA, USA.
James A WohlschlegelDepartment of Biological Chemistry, University of California Los Angeles, Los Angeles, CA, USA.ORCID 0000-0003-3399-901X
Steven E JacobsenDepartment of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA, USA. jacobsen@ucla.edu.ORCID 0000-0001-9483-138X

Funding

Bill and Melinda Gates Foundation (Bill & Melinda Gates Foundation) OPP1125410
6 · The paper itself

Abstract

Patterning of DNA methylation in eukaryotic genomes is controlled by de novo methylation, maintenance mechanisms and demethylation pathways. In Arabidopsis thaliana, DNA demethylation enzymes are clearly important for shaping methylation patterns, but how they are regulated is poorly understood. Here we show that the targeting of histone H3 lysine four trimethylation (H3K4me3) with the catalytic domain of the SDG2 histone methyltransferase potently erased DNA methylation and gene silencing at FWA and also erased CG DNA methylation in many other regions of the Arabidopsis genome. This methylation erasure was completely blocked in the ros1 dml2 dml3 triple mutant lacking DNA demethylation enzymes, showing that H3K4me3 promotes the active removal of DNA methylation. Conversely, we found that the targeted removal of H3K4me3 increased the efficiency of targeted DNA methylation. These results highlight H3K4me3 as a potent anti-DNA methylation mark and also pave the way for development of more powerful epigenome engineering tools.

Indexed as

ArabidopsisArabidopsis ProteinsDNA MethylationGene Expression Regulation, PlantHistone DemethylasesHistonesHistone-Lysine N-MethyltransferaseLysineMethylationArabidopsis ProteinsHistone Demethylaseshistone H3 trimethyl Lys4Histone-Lysine N-MethyltransferaseHistonesLysine

Identifiers

PMID39934332
PMCPMC11842272

What OpenQuestion holds

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.