PreprintCited by 16Epigenetics and DNA MethylationGenomics and Chromatin DynamicsCancer-related gene regulation

The DOI matches its Crossref record; 58 of the 58 references it cites were found in a registry or an index.

Molecular Mechanisms of DNMT3A-3L-Mediated de novo DNA Methylation on Chromatin

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Preprint — published as 10.1038/s41594-025-01704-4 · Paper page

Abstract

De novo DNA methylation is a fundamental epigenetic process essential for early development. It is mediated by DNA methyltransferase DNMT3A and DNMT3B, in cooperation with catalytically inactive DNMT3L. Abnormal DNA methylation contributes to genomic instability and oncogenesis, yet the mechanisms governing its establishment and regulation remain unclear. Here, we present high-resolution cryo-EM structures of the nucleosome-bound full-length DNMT3A2-3L and its oligomeric assemblies in the nucleosome-free state. Strikingly, DNMT3L C-terminal “Switching Helix” displayed a distinct conformation with a 180° rotational difference compared to its DNMT3B3 counterpart in the presence of nucleosome, preventing direct interactions with the nucleosome acidic patch. Instead, DNMT3L ADD domain promotes nucleosome binding, while DNMT3A PWWP domain inhibits it, indicating multi-layer regulation. Additionally, the novel oligomeric arrangement of DNMT3A2-3L in nucleosome-free states highlights its dynamic assembly and potential allosteric regulation. Furthermore, we identified the critical role of DNMT3L as a sensor of histone modifications, guiding the complex’s chromatin interaction. These findings uncover a previously unknown mechanism by which DNMT3A-3L mediates de novo DNA methylation on chromatin through complex reorganization, histone tail sensing, dynamic DNA search, and nucleosome engagement, providing key insights into epigenetic regulation.

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Crossref · 10.1101/2025.06.10.658647

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  1. 10.1038/nsb759 · DOI
  2. 10.1007/3-540-31390-7_7 · DOI
  3. 10.1093/nar/gky691 · DOI

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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
Venue
Nature Structural & Molecular Biology
Publisher
openRxiv
Published
2025-06-13
Volume
33
Issue
1
Pages
171-183
ISSN
1545-9985 (ISSN-L)
OpenAlex
W4415731750
Cited by
14
References
58
Citations by year
2026: 14
FWCI
4.18
Type
journal article
Language
en
Open access
Locations
  • Nature Structural & Molecular Biology (publishedVersion)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
  • PubMed (publishedVersion)
  • PubMed Central (publishedVersion)
  • PubMed Central (submittedVersion)
Funders
  • the Doisy Fund of the Edward A. Doisy Department of Biochemistry and Molecular Biology at Saint Louis University School of Medicine
  • National Institutes of Health (R35CA209859, R35GM147261, R50CA243878)
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

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