Evidence map›Paper›PMID 41006297›Full record

ArticleNature communications2025

Cryo-EM reveals evolutionarily conserved and distinct structural features of plant CG maintenance methyltransferase MET1.

Amika Kikuchi, Atsuya Nishiyama, Yoshie Chiba, Makoto Nakanishi, Taiko Kim To, Kyohei Arita

Abstract read
In one paragraph

Article in Nature communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing 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

4 citing papers in PubMed.

  1. Article
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  3. 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

6 authors.

Amika KikuchiStructural Biology Laboratory, Graduate School of Medical Life Science, Yokohama City University, Yokohama, Kanagawa, Japan.ORCID http://orcid.org/0000-0002-5112-0868
Atsuya NishiyamaDivision of Cancer Cell Biology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.ORCID http://orcid.org/0000-0002-8416-3776
Yoshie ChibaDivision of Cancer Cell Biology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
Makoto NakanishiDivision of Cancer Cell Biology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.ORCID http://orcid.org/0000-0002-6707-3584
Taiko Kim ToLife Science and Technology, Institute of Science Tokyo, Yokohama, Kanagawa, Japan.ORCID http://orcid.org/0000-0003-1255-6930
Kyohei AritaStructural Biology Laboratory, Graduate School of Medical Life Science, Yokohama City University, Yokohama, Kanagawa, Japan. aritak@yokohama-cu.ac.jp.ORCID http://orcid.org/0000-0002-9762-8405

Funding

MEXT | Japan Society for the Promotion of Science (JSPS) 19H05741 and 24K01967, 24K21950, and 25H01301
6 · The paper itself

Abstract

DNA methylation is essential for genomic function and transposable element silencing. In plants, DNA methylation occurs in CG, CHG, and CHH contexts (where H = A, T, or C), with the maintenance of CG methylation mediated by the DNA methyltransferase MET1. The molecular mechanism by which MET1 maintains CG methylation, however, remains unclear. Here, we report cryogenic electron microscopy structures of Arabidopsis thaliana MET1. We find that the methyltransferase domain of MET1 specifically methylates hemimethylated DNA in vitro. The structure of MET1 bound to hemimethylated DNA reveals the activation mechanism of MET1 resembling that of mammalian DNMT1. Curiously, the structure of apo-MET1 shows an autoinhibitory state distinct from that of DNMT1, where the RFTS2 domain and the connecting linker inhibit DNA binding. The autoinhibition of MET1 is relieved upon binding of a potential activator, ubiquitinated histone H3. Taken together, our structural analysis demonstrates both conserved and distinct molecular mechanisms regulating CG maintenance methylation in plant and animal DNA methyltransferases.

Indexed as

ArabidopsisArabidopsis ProteinsDNA (Cytosine-5-)-MethyltransferasesDNA MethylationCryoelectron MicroscopyDNA (Cytosine-5-)-Methyltransferase 1DNA, PlantEvolution, MolecularHistonesModels, MolecularProtein BindingProtein DomainsArabidopsis ProteinsDNA (Cytosine-5-)-Methyltransferase 1DNA (Cytosine-5-)-MethyltransferasesDNA, PlantHistonesMET1 protein, Arabidopsis

Identifiers

PMID41006297
PMCPMC12474915

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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.