Evidence map›Paper›PMID 42380212›Full record

ArticleNature communications2026

Antagonistic histone H2A variants and autonomous heterochromatin formation shape epigenomic patterns in Arabidopsis.

Shoko Oda, Sayaka Tominaga, Shumpei Takeuchi, Akihisa Osakabe, Akira Kawabe, Frédéric Berger, Tetsuji Kakutani, Taiko Kim To

Abstract read
In one paragraph

Article in Nature communications, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing 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

1 citing paper in PubMed.

  1. Article
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

8 authors.

Shoko OdaSchool of Life Science and Technology, Institute of Science Tokyo, Yokohama, Japan.
Sayaka TominagaSchool of Life Science and Technology, Institute of Science Tokyo, Yokohama, Japan.
Shumpei TakeuchiSchool of Life Science and Technology, Institute of Science Tokyo, Yokohama, Japan.
Akihisa OsakabeDepartment of Biological Sciences, The University of Tokyo, Bunkyo, Japan.
Akira KawabeFaculty of Life Sciences, Kyoto Sangyo University, Kyoto, Japan.ORCID http://orcid.org/0000-0001-5770-412X
Frédéric BergerGregor Mendel Institute (GMI), Vienna Biocenter (VBC), Austrian Academy of Sciences, Vienna, Austria.ORCID http://orcid.org/0000-0002-3609-8260
Tetsuji KakutaniDepartment of Biological Sciences, The University of Tokyo, Bunkyo, Japan.ORCID http://orcid.org/0000-0002-6137-4474
Taiko Kim ToSchool of Life Science and Technology, Institute of Science Tokyo, Yokohama, Japan. to.t.1057@m.isct.ac.jp.ORCID http://orcid.org/0000-0003-1255-6930

Funding

MEXT | Japan Science and Technology Agency (JST) JPMJFR224XMEXT | Japan Society for the Promotion of Science (JSPS) 17K15059MEXT | Japan Society for the Promotion of Science (JSPS) 19H05740MEXT | Japan Society for the Promotion of Science (JSPS) 21H04977MEXT | Japan Society for the Promotion of Science (JSPS) 22K06180MEXT | Japan Society for the Promotion of Science (JSPS) 23KJ0740MEXT | Japan Society for the Promotion of Science (JSPS) 24K02002MEXT | Japan Society for the Promotion of Science (JSPS) 24K02077MEXT | Japan Society for the Promotion of Science (JSPS) 25H01299MEXT | Japan Society for the Promotion of Science (JSPS) 25H01300MEXT | Japan Society for the Promotion of Science (JSPS) 25H02544MEXT | Japan Society for the Promotion of Science (JSPS) 25K02258MEXT | JST | Core Research for Evolutional Science and Technology (CREST) JPMJCR20SMEXT | JST | Precursory Research for Embryonic Science and Technology (PRESTO) JPMJPR20K3
6 · The paper itself

Abstract

Heterochromatin formation is pivotal in many eukaryotes with repetitive sequences, such as transposable elements (TEs). However, in plants, where the known de novo DNA methylation mechanism (RdDM) targets euchromatin, how heterochromatin is formed in a region-specific manner remains unclear. We previously reported an RdDM-independent de novo establishment of H3K9me and non-CpG methylation, both of which localize in heterochromatin. Here we show that the mutually exclusive histone H2A variants, H2A.W and H2A.Z, function as guides to initiate heterochromatin formation; H2A.W and H2A.Z promotes and inhibits heterochromatin establishment, respectively, especially in chromosomal arm regions with dispersed TEs. In contrast, pericentromeric TEs demonstrate autonomous heterochromatin formation, less dependently on these H2A variants. Furthermore, H2A.Z protects protein-coding genes from ectopic heterochromatin formation, possibly by preventing its spreading. We propose that the genome indexing mechanism driven by H2A variants, as well as the autonomous formation of pericentromeric heterochromatin, shapes proper epigenomic patterns in Arabidopsis.

Indexed as

ArabidopsisArabidopsis ProteinsEpigenesis, GeneticHeterochromatinHistonesDNA MethylationDNA Transposable ElementsEpigenomicsEuchromatinGene Expression Regulation, PlantArabidopsis ProteinsDNA Transposable ElementsEuchromatinHeterochromatinHistones

Identifiers

PMID42380212
PMCPMC13457619

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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.