Evidence map›Paper›PMID 41449196›Full record

ArticleNature communications2025

Germline epigenome editing identifies H3K9me3 as a mediator of intergenerational DNA methylation recovery in mice.

Takuro Horii, Sumiyo Morita, Shinjiro Hino, Yuko Hino, Hiroto S Fukushima, Ryosuke Kobayashi, Mika Kimura, Mitsuyoshi Nakao, Yoichi Mizukami, Azusa Inoue and 1 more

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
  2. Review
  3. Article
  4. Review
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.

Takuro HoriiLaboratory of Genome Science, Biosignal Genome Resource Center, Institute for Molecular and Cellular Regulation, Gunma University, Maebashi, Japan. horii@gunma-u.ac.jp.ORCID http://orcid.org/0009-0004-2167-1791
Sumiyo MoritaLaboratory of Genome Science, Biosignal Genome Resource Center, Institute for Molecular and Cellular Regulation, Gunma University, Maebashi, Japan.
Shinjiro HinoDepartment of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, Japan.
Yuko HinoDepartment of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, Japan.
Hiroto S FukushimaLaboratory for Epigenome Inheritance, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.ORCID http://orcid.org/0009-0003-0736-3680
Ryosuke KobayashiLaboratory of Genome Science, Biosignal Genome Resource Center, Institute for Molecular and Cellular Regulation, Gunma University, Maebashi, Japan.ORCID http://orcid.org/0009-0009-8666-1312
Mika KimuraLaboratory of Genome Science, Biosignal Genome Resource Center, Institute for Molecular and Cellular Regulation, Gunma University, Maebashi, Japan.
Mitsuyoshi NakaoDepartment of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, Japan.
Yoichi MizukamiInstitute of Gene Research, Yamaguchi University Science Research Center, Yamaguchi, Japan.ORCID http://orcid.org/0000-0002-3290-0754
Azusa InoueLaboratory for Epigenome Inheritance, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.ORCID http://orcid.org/0000-0002-9703-0358
Izuho HatadaLaboratory of Genome Science, Biosignal Genome Resource Center, Institute for Molecular and Cellular Regulation, Gunma University, Maebashi, Japan. hatada@gunma-u.ac.jp.ORCID http://orcid.org/0000-0001-7225-3929

Funding

Japan Agency for Medical Research and Development (AMED) 21ek0109489h0002Japan Agency for Medical Research and Development (AMED) 22gm6310009h0004Japan Agency for Medical Research and Development (AMED) JP21am0101120 and JP24ama121049MEXT | Japan Science and Technology Agency (JST) JPMJFR2335MEXT | Japan Society for the Promotion of Science (JSPS) 23K05727, Scientific Research (C)MEXT | Japan Society for the Promotion of Science (JSPS) 23K23802, Scientific Research (B)MEXT | Japan Society for the Promotion of Science (JSPS) 24K02582, Scientific Research (B)MEXT | Japan Society for the Promotion of Science (JSPS) 24KJ0236MEXT | Japan Society for the Promotion of Science (JSPS) 25H01355
6 · The paper itself

Abstract

Inter/transgenerational epigenetic inheritance is a crucial and controversial theory that could reshape the concept of genetics. To investigate this theory directly, we invent a system for targeted reprogramming of epigenetic memory in mouse sperm. Using this system, we erase DNA methylation at the differentially methylated region of the H19 gene (H19-DMR) in sperm, which causes Silver-Russell syndrome-like phenotypes in F1 offspring. Although DNA methylation is fully lost in the sperm, it is partially restored during pre-implantation development, suggesting the existence of epigenetic memory that instructs de novo DNA methylation. Importantly, targeted removal of histone modifications in zygotes reveals that tri-methylation at lysine 9 of histone H3 (H3K9me3), which is deposited shortly after fertilization, is required for the subsequent de novo DNA methylation at the H19-DMR. Thus, our study provides a robust germline editing tool, which reveals partial intergenerational inheritance and no transgenerational inheritance at the model locus. Furthermore, we identify H3K9me3 as a mediator for DNA methylation recovery also acting at imprinted loci.

Indexed as

DNA MethylationEpigenesis, GeneticEpigenomeGene EditingHistonesAnimalsEpigenome EditingFemaleGenomic ImprintingGerm CellsMaleMiceMice, Inbred C57BLRNA, Long NoncodingSpermatozoaZygoteH19 long non-coding RNAHistonesRNA, Long Noncoding

Identifiers

PMID41449196
PMCPMC12741052

What Socratic holds

Textmetadata
LicenceCC BY-NC-ND
Read underepoch 390

Registered trials

None linked

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 Socratic graph.