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


Metabolic reprogramming occurs in response to the cellular environment to mediate differentiation1,2,3, but the fundamental mechanisms linking metabolic processes to differentiation programs remain to be elucidated. During osteoclast differentiation, a shift toward more oxidative metabolic processes occurs3. 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 osteoclastogenesis4,5,6,7, 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.

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Figure 1: Osteoclast-specific Dnmt3a-deficient mice exhibit a high bone mass phenotype.
Figure 2: Deficiency of Dnmt3a impairs osteoclastogenesis and protects against pathological bone loss.
Figure 3: DNA methylation by Dnmt3a downregulates Irf8 gene expression.
Figure 4: RANKL induces a metabolic shift toward oxidative metabolic processes in osteoclasts.

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We thank K. Kaseda, M. Shirazaki, and Y. Maijima for technical assistance and J. Kikuta, S. Fujimori, and S. Simmons for helpful discussions. We also thank M. Okano, S. Takeda, and G. Karsenty; H. Wu, M. Takami, and K. Ozato for the gifts of Dnmt3a-deficient ESCs, Col1a1–Cre transgenic mice, the Dnmt3a expression vector, and Irf8−/− mice, respectively. This work was supported by Grants-in-Aid for Scientific Research on Innovative Areas from the Japan Society for the Promotion of Science (JSPS) (26116719; K.N.); Grants-in-Aid for Creative Scientific Research and Young Scientists (A) from the JSPS (26713010; K.N.); Grants-in-Aid for Scientific Research (A) from the JSPS (25253070; M.I.); the Funding Program for World-Leading Innovative R&D on Science and Technology (FIRST Program) from the Ministry of Education, Culture, Sports, Science and Technology, Japan (MEXT; M.I.); the Platform for Drug Discovery, Informatics, and Structural Life Science from the MEXT, Japan (T.T., S. Kawaguchi and M.Y.); and grants from the Astellas Foundation for Research on Metabolic Disorders (K.N.), the Ichiro Kanehara Foundation (K.N.), the Shimadzu Science Foundation (K.N.), the Takeda Science Foundation (K.N. and M.I.), and the International Human Frontier Science Program (RGY0077/2011 to M.I.).

Author information




K.N. directed the project, conducted most of the experiments, and prepared the manuscript. Y.I. contributed to in vitro analyses. Y.K. supported the generation of osteoclast-specific Dnmt3a knockout mice. F.K. and M.Y. contributed to MBD-seq analyses. S. Kawaguchi and T.T. contributed to in silico analyses. T.N. and S. Kato generated CtskCre/+ mice. H.T. supported the GeneChip analysis. M.I. helped to direct the project and prepare the manuscript.

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Correspondence to Keizo Nishikawa or Masaru Ishii.

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The authors declare no competing financial interests.

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Nishikawa, K., Iwamoto, Y., Kobayashi, Y. et al. DNA methyltransferase 3a regulates osteoclast differentiation by coupling to an S-adenosylmethionine–producing metabolic pathway. Nat Med 21, 281–287 (2015). https://doi.org/10.1038/nm.3774

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