CoChat
Sign Up
Cited by 14Epigenetics and DNA MethylationGenomics and Chromatin DynamicsCancer-related gene regulation

The DOI matches its Crossref record; 6 of the 6 references it cites were found in a registry or an index.

Mechanisms of DNMT3A–3L-mediated de novo DNA methylation on chromatin

Open access
Yan, Yan, Zhou, X. Edward, Thomas, Stacey L., Liu, Minmin, Lai, Gan-Qiang, Worden, Evan J., Jones, Peter A., Xu, Ting-Hai·2026·Nature Structural & Molecular Biology
DOI 10.1038/s41594-025-01704-4PMC PMC13049598

Published version of a preprint

Open this paper in CoChat — free accountOpen PDF

Abstract

De novo DNA methylation is mediated by DNA methyltransferases DNMT3A and DNMT3B, in cooperation with the catalytically inactive paralogs DNMT3L and DNMT3B3. DNMT3L is predominantly expressed in embryonic stem cells to establish methylation patterns and is silenced upon differentiation, with DNMT3B3 substituting in somatic cells. Here we present high-resolution cryo-electron microscopy structures of nucleosome-bound, full-length DNMT3A2-3L and its oligomeric assemblies in the nucleosome-free state. We identified the critical role of DNMT3L as a histone modification sensor, guiding chromatin engagement through a mechanism distinct from DNMT3B3. The structures show a 180° rotated 'switching helix' in DNMT3L that prevents direct interaction with the nucleosome acidic patch. Instead, nucleosome binding is mediated by the DNMT3L ADD domain, while the DNMT3A PWWP domain exhibits reduced engagement in the absence of H3K36 methylation. The oligomeric arrangement of DNMT3A2-3L in nucleosome-free states highlights its dynamic assembly and potential allosteric regulation. We further capture dynamic structural movements of DNMT3A2-3L on nucleosomes. These findings uncover a previously unknown mechanism by which DNMT3A-3L mediates de novo DNA methylation on chromatin through complex assembly, histone tail sensing, dynamic DNA search and regulated nucleosome engagement, providing insights into epigenetic regulation.

Overview

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1038/s41594-025-01704-4

Cites

6 of 6 references verified0 citation errors · 0 not checkable

Statistics

Verification

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Citations

Cites

Flagged first, then by citations

Research works printed but not linked: 55

  1. Okano, M., Bell, D. W., Haber, D. A. & Li, E. DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development. Cell 99, 247–257 (1999). · DOI · Paper page
  2. Greenberg, M. V. C. & Bourc’his, D. The diverse roles of DNA methylation in mammalian development and disease. Nat. Rev. Mol. Cell Biol. 20, 590–607 (2019). · DOI
  3. Hata, K., Okano, M., Lei, H. & Li, E. Dnmt3L cooperates with the Dnmt3 family of de novo DNA methyltransferases to establish maternal imprints in mice. Development 129, 1983–1993 (2002). · DOI
  4. Duymich, C. E., Charlet, J., Yang, X., Jones, P. A. & Liang, G. DNMT3B isoforms without catalytic activity stimulate gene body methylation as accessory proteins in somatic cells. Nat. Commun. 7, 11453 (2016). · DOI
  5. Zeng, Y. et al. The inactive Dnmt3b3 isoform preferentially enhances Dnmt3b-mediated DNA methylation. Genes Dev. 34, 1546–1558 (2020). · DOI
  6. Zhang, Z. M. et al. Structural basis for DNMT3A-mediated de novo DNA methylation. Nature 554, 387–391 (2018). · DOI
  7. Klimasauskas, S., Kumar, S., Roberts, R. J. & Cheng, X. HhaI methyltransferase flips its target base out of the DNA helix. Cell 76, 357–369 (1994). · DOI
  8. Jia, D., Jurkowska, R. Z., Zhang, X., Jeltsch, A. & Cheng, X. Structure of Dnmt3a bound to Dnmt3L suggests a model for de novo DNA methylation. Nature 449, 248–251 (2007). · DOI
  9. Ooi, S. K. et al. DNMT3L connects unmethylated lysine 4 of histone H3 to de novo methylation of DNA. Nature 448, 714–717 (2007). · DOI
  10. Xu, T. H. et al. Structure of nucleosome-bound DNA methyltransferases DNMT3A and DNMT3B. Nature 586, 151–155 (2020). · DOI
  11. Veland, N. et al. DNMT3L facilitates DNA methylation partly by maintaining DNMT3A stability in mouse embryonic stem cells. Nucleic Acids Res. 47, 152–167 (2019). · DOI
  12. Chen, B. F., Gu, S., Suen, Y. K., Li, L. & Chan, W. Y. microRNA-199a-3p, DNMT3A, and aberrant DNA methylation in testicular cancer. Epigenetics 9, 119–128 (2014). · DOI
  13. Davies, H. R. et al. Epigenetic modifiers DNMT3A and BCOR are recurrently mutated in CYLD cutaneous syndrome. Nat. Commun. 10, 4717 (2019). · DOI
  14. Chen, T., Tsujimoto, N. & Li, E. The PWWP domain of Dnmt3a and Dnmt3b is required for directing DNA methylation to the major satellite repeats at pericentric heterochromatin. Mol. Cell Biol. 24, 9048–9058 (2004). · DOI
  15. Dhayalan, A. et al. The Dnmt3a PWWP domain reads histone 3 lysine 36 trimethylation and guides DNA methylation. J. Biol. Chem. 285, 26114–26120 (2010). · DOI
  16. Dukatz, M. et al. H3K36me2/3 binding and DNA binding of the DNA methyltransferase DNMT3A PWWP domain both contribute to its chromatin interaction. J. Mol. Biol. 431, 5063–5074 (2019). · DOI
  17. Qiu, C., Sawada, K., Zhang, X. & Cheng, X. The PWWP domain of mammalian DNA methyltransferase Dnmt3b defines a new family of DNA-binding folds. Nat. Struct. Biol. 9, 217–224 (2002).
  18. Otani, J. et al. Structural basis for recognition of H3K4 methylation status by the DNA methyltransferase 3A ATRX–DNMT3–DNMT3L domain. EMBO Rep. 10, 1235–1241 (2009). · DOI
  19. Zhang, Y. et al. Chromatin methylation activity of Dnmt3a and Dnmt3a/3L is guided by interaction of the ADD domain with the histone H3 tail. Nucleic Acids Res. 38, 4246–4253 (2010). · DOI
  20. Jeltsch, A. Molecular enzymology of mammalian DNA methyltransferases. Curr. Top. Microbiol. Immunol. 301, 203–225 (2006).
  21. Suetake, I., Shinozaki, F., Miyagawa, J., Takeshima, H. & Tajima, S. DNMT3L stimulates the DNA methylation activity of Dnmt3a and Dnmt3b through a direct interaction. J. Biol. Chem. 279, 27816–27823 (2004). · DOI
  22. Lowary, P. T. & Widom, J. New DNA sequence rules for high affinity binding to histone octamer and sequence-directed nucleosome positioning. J. Mol. Biol. 276, 19–42 (1998). · DOI
  23. Chedin, F., Lieber, M. R. & Hsieh, C. L. The DNA methyltransferase-like protein DNMT3L stimulates de novo methylation by Dnmt3a. Proc. Natl Acad. Sci. USA 99, 16916–16921 (2002). · DOI
  24. Gowher, H., Liebert, K., Hermann, A., Xu, G. & Jeltsch, A. Mechanism of stimulation of catalytic activity of Dnmt3A and Dnmt3B DNA-(cytosine-C5)-methyltransferases by Dnmt3L. J. Biol. Chem. 280, 13341–13348 (2005). · DOI
  25. Holz-Schietinger, C., Matje, D. M., Harrison, M. F. & Reich, N. O. Oligomerization of DNMT3A controls the mechanism of de novo DNA methylation. J. Biol. Chem. 286, 41479–41488 (2011). · DOI
  26. Lu, J. et al. Structure-guided functional suppression of AML-associated DNMT3A hotspot mutations. Nat. Commun. 15, 3111 (2024). · DOI
  27. Jurkowska, R. Z. et al. Oligomerization and binding of the Dnmt3a DNA methyltransferase to parallel DNA molecules: heterochromatic localization and role of Dnmt3L. J. Biol. Chem. 286, 24200–24207 (2011). · DOI
  28. Lu, J. et al. Structural basis for the allosteric regulation and dynamic assembly of DNMT3B. Nucleic Acids Res. 51, 12476–12491 (2023). · DOI
  29. Ren, W. et al. DNMT1 reads heterochromatic H4K20me3 to reinforce LINE-1 DNA methylation. Nat. Commun. 12, 2490 (2021). · DOI
  30. Gretarsson, K. H. et al. Cancer-associated DNA hypermethylation of Polycomb targets requires DNMT3A dual recognition of histone H2AK119 ubiquitination and the nucleosome acidic patch. Sci. Adv. 10, eadp0975 (2024). · DOI
  31. Wapenaar, H. et al. The N-terminal region of DNMT3A engages the nucleosome surface to aid chromatin recruitment. EMBO Rep. 25, 5743–5779 (2024). · DOI
  32. Chen, X. et al. Structural basis for the H2AK119ub1-specific DNMT3A–nucleosome interaction. Nat. Commun. 15, 6217 (2024). · DOI
  33. Wang, H. & Helin, K. Roles of H3K4 methylation in biology and disease. Trends Cell Biol. 35, 115–128 (2025). · DOI
  34. Li, B. Z. et al. Histone tails regulate DNA methylation by allosterically activating de novo methyltransferase. Cell Res. 21, 1172–1181 (2011). · DOI
  35. Choi, W., Li, C., Chen, Y., Wang, Y. & Cheng, Y. Structural dynamics of human fatty acid synthase in the condensing cycle. Nature 641, 529–536 (2025). · DOI
  36. Jeltsch, A. & Jurkowska, R. Z. Allosteric control of mammalian DNA methyltransferases—a new regulatory paradigm. Nucleic Acids Res. 44, 8556–8575 (2016). · DOI
  37. Lovkvist, C., Dodd, I. B., Sneppen, K. & Haerter, J. O. DNA methylation in human epigenomes depends on local topology of CpG sites. Nucleic Acids Res. 44, 5123–5132 (2016). · DOI
  38. Jeltsch, A. & Jurkowska, R. Z. Multimerization of the dnmt3a DNA methyltransferase and its functional implications. Prog. Mol. Biol. Transl. Sci. 117, 445–464 (2013). · DOI
  39. Nguyen, T. V. et al. The R882H DNMT3A hot spot mutation stabilizes the formation of large DNMT3A oligomers with low DNA methyltransferase activity. J. Biol. Chem. 294, 16966–16977 (2019). · DOI
  40. Ehrlich, M. & Wang, R. Y. 5-Methylcytosine in eukaryotic DNA. Science 212, 1350–1357 (1981). · DOI
  41. Chen, Z. X., Mann, J. R., Hsieh, C. L., Riggs, A. D. & Chedin, F. Physical and functional interactions between the human DNMT3L protein and members of the de novo methyltransferase family. J. Cell Biochem. 95, 902–917 (2005). · DOI
  42. Brohm, A. et al. Methylation of recombinant mononucleosomes by DNMT3A demonstrates efficient linker DNA methylation and a role of H3K36me3. Commun. Biol. 5, 192 (2022). · DOI
  43. Lay, F. D. et al. The role of DNA methylation in directing the functional organization of the cancer epigenome. Genome Res. 25, 467–477 (2015). · DOI
  44. Bouazoune, K., Miranda, T. B., Jones, P. A. & Kingston, R. E. Analysis of individual remodeled nucleosomes reveals decreased histone–DNA contacts created by hSWI/SNF. Nucleic Acids Res. 37, 5279–5294 (2009). · DOI
  45. Kastner, B. et al. GraFix: sample preparation for single-particle electron cryomicroscopy. Nat. Methods 5, 53–55 (2008). · DOI
  46. Stark, H. GraFix: stabilization of fragile macromolecular complexes for single particle cryo-EM. Methods Enzymol. 481, 109–126 (2010). · DOI
  47. Mastronarde, D. N. Automated electron microscope tomography using robust prediction of specimen movements. J. Struct. Biol. 152, 36–51 (2005). · DOI
  48. Sanchez-Garcia, R. et al. DeepEMhancer: a deep learning solution for cryo-EM volume post-processing. Commun. Biol. 4, 874 (2021). · DOI
  49. Evans R. et al. Protein complex prediction with AlphaFold-Multimer. Preprint at bioRxiv https://doi.org/10.1101/2021.10.04.463034 (2022). · DOI · Paper page
  50. Pettersen, E. F. et al. UCSF ChimeraX: structure visualization for researchers, educators, and developers. Protein Sci. 30, 70–82 (2021). · DOI
  51. Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D Biol. Crystallogr. 60, 2126–2132 (2004). · DOI · Paper page
  52. Adams, P. D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D Biol. Crystallogr. 66, 213–221 (2010). · DOI · Paper page
  53. Chadda, R. et al. Partial wrapping of single-stranded DNA by replication protein A and modulation through phosphorylation. Nucleic Acids Res. 52, 11626–11640 (2024). · DOI
  54. Zhou, W., Triche, T. J. Jr., Laird, P. W. & Shen, H. SeSAMe: reducing artifactual detection of DNA methylation by Infinium BeadChips in genomic deletions. Nucleic Acids Res. 46, e123 (2018).
  55. Tiedemann, R. L. et al. UHRF1 ubiquitin ligase activity supports the maintenance of low-density CpG methylation. Nucleic Acids Res. 52, 13733–13756 (2024). · DOI

Metadata

Authors
Yan, Y., Zhou, X. E., Thomas, S. L., Liu, M., Lai, G.-Q., Worden, E. J., Jones, P. A., & Xu, T.-H.
Affiliations
  • Saint Louis University (US)
  • Van Andel Institute (US)
Corresponding author
  • Jones, Peter A.
  • Xu, Ting-Hai
ORCID
Venue
Nature Structural & Molecular Biology
Publisher
Springer Science and Business Media LLC
Published
2025-10-31
Volume
33
Issue
1
Pages
171-183
ISSN
  • 1545-9985 (ISSN-L)
  • 1545-9993
DOI
10.1038/s41594-025-01704-4
PMC
PMC13049598
OpenAlex
W4415731750
Cited by
14
References
6
Citations by year
2026: 14
FWCI
3.87
Type
journal article
Language
en
Open access
Licence
Locations
  • Nature Structural & Molecular Biology (publishedVersion)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
  • PubMed (publishedVersion)
  • PubMed Central (publishedVersion)
  • PubMed Central (submittedVersion)
Funders
  • Saint Louis University
  • National Institutes of Health
  • University of California, San Francisco
  • National Cancer Institute (R35CA209859, R50CA243878)
  • National Institute of General Medical Sciences (R35GM147261)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Cancer-related gene regulation
Keywords
DNMT3A, DNMT3L, de novo methylation, DNA methyltransferases, nucleosome binding, H3K36 methylation, PWWP domain, protein oligomerization, allosteric regulation, cryo-EM structure

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review