Evidence map›Paper›PMID 25706873›Full record

ArticleNature medicine2015

DNA methyltransferase 3a regulates osteoclast differentiation by coupling to an S-adenosylmethionine-producing metabolic pathway.

Keizo Nishikawa, Yoriko Iwamoto, Yasuhiro Kobayashi, Fumiki Katsuoka, Shin-ichi Kawaguchi, Tadayuki Tsujita, Takashi Nakamura, Shigeaki Kato, Masayuki Yamamoto, Hiroshi Takayanagi and 1 more

Abstract read
PubMed Publisher
In one paragraph

Article in Nature medicine, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 139 papers, 2 of them syntheses that pooled it.

0numbers the graph read from it
0cells of the map it votes in
139citing papers in PubMed, 2 pooled it
10.8field-weighted citation impact, top 1% of its field
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

139 citing papers in PubMed, 2 syntheses or guidelines pooled it, 221 citations in OpenAlex.

  1. Pooled it
  2. Interplay Between Glucose Metabolism and Chromatin Modifications in Cancer.Frontiers in cell and developmental biology · 2021
    Pooled it
  3. Article
  4. Article
  5. Review
  6. Article
  7. Methionine restriction and mimetics to ameliorate human aging and disease.Trends in endocrinology and metabolism: TEM · 2026
    Review
  8. Article
  9. Article
  10. Article
  11. Review
  12. Review
  13. Review
  14. Article
  15. Article
  16. Dnmt3a-mediated hypermethylation of FoxO3 promotes redox imbalance during osteoclastogenesis.Proceedings of the National Academy of Sciences of the United States of America · 2025
    Article
  17. Review
  18. Article
  19. Article
  20. Review

79 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

11 authors at 7 institutions in 1 country.

Keizo Nishikawa1] Department of Immunology and Cell Biology, Graduate School of Medicine and Frontier Biosciences, Osaka University, Osaka, Japan. [2] WPI-Immunology Frontier Research Center, Osaka University, Osaka, Japan. [3] Japan Science and Technology Agency, CREST, Tokyo, Japan.
Yoriko Iwamoto1] Department of Immunology and Cell Biology, Graduate School of Medicine and Frontier Biosciences, Osaka University, Osaka, Japan. [2] WPI-Immunology Frontier Research Center, Osaka University, Osaka, Japan. [3] Japan Science and Technology Agency, CREST, Tokyo, Japan. [4] Department of Otorhinolaryngology-Head and Neck Surgery, Graduate School of Medicine, Osaka University, Osaka, Japan.
Yasuhiro KobayashiInstitute for Oral Science, Matsumoto Dental University, Nagano, Japan.
Fumiki Katsuoka1] Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan. [2] Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Japan.
Shin-ichi KawaguchiDepartment of Molecular Medicine and Therapy, Tohoku University Graduate School of Medicine, Sendai, Japan.ORCID 0000000291003885
Tadayuki TsujitaDepartment of Medical Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Japan.
Takashi NakamuraDepartment of Biochemistry, School of Medicine, Keio University, Tokyo, Japan.
Shigeaki KatoSoma Central Hospital, Fukushima, Japan.
Masayuki Yamamoto1] Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan. [2] Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Japan.
Hiroshi Takayanagi1] Department of Immunology, Graduate School of Medicine and Faculty of Medicine, University of Tokyo, Tokyo, Japan. [2] Japan Science and Technology Agency, ERATO, Takayanagi Osteonetwork Project, Tokyo, Japan.
Masaru Ishii1] Department of Immunology and Cell Biology, Graduate School of Medicine and Frontier Biosciences, Osaka University, Osaka, Japan. [2] WPI-Immunology Frontier Research Center, Osaka University, Osaka, Japan. [3] Japan Science and Technology Agency, CREST, Tokyo, Japan.
Tohoku University · JPUbe Frontier University · JPJapan Science and Technology Agency · JPKeio University · JPMatsumoto Dental University · JPSoma Central Hospital · JPThe University of Osaka · JP

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Metabolic reprogramming occurs in response to the cellular environment to mediate differentiation, but the fundamental mechanisms linking metabolic processes to differentiation programs remain to be elucidated. During osteoclast differentiation, a shift toward more oxidative metabolic processes occurs. In this study we identified the de novo DNA methyltransferase 3a (Dnmt3a) as a transcription factor that couples these metabolic changes to osteoclast differentiation. We also found that receptor activator of nuclear factor-κB ligand (RANKL), an essential cytokine for osteoclastogenesis, induces this metabolic shift towards oxidative metabolism, which is accompanied by an increase in S-adenosylmethionine (SAM) production. We found that SAM-mediated DNA methylation by Dnmt3a regulates osteoclastogenesis via epigenetic repression of anti-osteoclastogenic genes. The importance of Dnmt3a in bone homeostasis was underscored by the observations that Dnmt3a-deficient osteoclast precursor cells do not differentiate efficiently into osteoclasts and that mice with an osteoclast-specific deficiency in Dnmt3a have elevated bone mass due to a smaller number of osteoclasts. Furthermore, inhibition of DNA methylation by theaflavin-3,3'-digallate abrogated bone loss in models of osteoporosis. Thus, this study reveals the role of epigenetic processes in the regulation of cellular metabolism and differentiation, which may provide the molecular basis for a new therapeutic strategy for a variety of bone disorders.

Indexed as

AnimalsBiflavonoidsBone ResorptionCatechinCell DifferentiationDNA (Cytosine-5-)-MethyltransferasesDNA MethylationDNA Methyltransferase 3ADown-RegulationGene ExpressionMiceOsteoclastsOsteogenesisRANK LigandS-AdenosylmethionineTranscription FactorsBiflavonoidsCatechinDNA (Cytosine-5-)-MethyltransferasesDNA Methyltransferase 3ADnmt3a protein, mouseRANK LigandS-Adenosylmethioninetheaflavin-3,3'-digallateTnfsf11 protein, mouseTranscription Factors

Identifiers

PMID25706873
OpenAlexW1989944094

What OpenQuestion holds

Textmetadata
Read underepoch 390

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.