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TitleMechanisms of DNMT3A-3L-mediated de novo DNA methylation on chromatin.
Journal, issue, pagesNat Struct Mol Biol, Year 2025
Publish dateOct 31, 2025
AuthorsYan Yan / X Edward Zhou / Stacey L Thomas / Minmin Liu / Gan-Qiang Lai / Evan J Worden / Peter A Jones / Ting-Hai Xu /
PubMed AbstractDe 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 ...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.
External linksNat Struct Mol Biol / PubMed:41174279
MethodsEM (single particle)
Resolution3.08 - 3.66 Å
Structure data

EMDB-48322: The consensus cryo-EM map of nucleosome-bound DNA methyltransferases DNMT3A2 and DNMT3L
Method: EM (single particle) / Resolution: 3.1 Å

EMDB-48492: The methyltransferases-focused cryo-EM map of nucleosome-bound DNA methyltransferases DNMT3A2 and DNMT3L
Method: EM (single particle) / Resolution: 3.6 Å

EMDB-48493: The nucleosome-focused cryo-EM map of nucleosome-bound DNA methyltransferases DNMT3A2 and DNMT3L
Method: EM (single particle) / Resolution: 3.08 Å

EMDB-48494: The "up" state cryo-EM map of nucleosome-bound DNA methyltransferases DNMT3A2 and DNMT3L
Method: EM (single particle) / Resolution: 3.16 Å

EMDB-48495: The intermediate state cryo-EM map of nucleosome-bound DNA methyltransferases DNMT3A2 and DNMT3L
Method: EM (single particle) / Resolution: 3.29 Å

48496

9mp0

EMDB-48496, PDB-9mp0:
The cryo-EM structure of the human DNA methyltransferases DNMT3A2 and DNMT3L dodecamer
Method: EM (single particle) / Resolution: 3.66 Å

48497

9mpo

EMDB-48497, PDB-9mpo:
The cryo-EM structure of the human DNA methyltransferase DNMT3A2 and DNMT3L octamer
Method: EM (single particle) / Resolution: 3.62 Å

48498

9mpp

EMDB-48498, PDB-9mpp:
The cryo-EM structure of nucleosome-bound DNA methyltransferases DNMT3A2 and DNMT3L
Method: EM (single particle) / Resolution: 3.1 Å

Chemicals

ChemComp-ZN:
Unknown entry

ChemComp-SAH:
S-ADENOSYL-L-HOMOCYSTEINE

Source
  • xenopus laevis (African clawed frog)
  • homo sapiens (human)
  • synthetic construct (others)
KeywordsDNA BINDING PROTEIN / methyltransferase / dodecamer / TRANSFERASE / TRANSFERASE-DNA complex / octamer / DNMT-nucleosome complex

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