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TitleThe N-terminal region of DNMT3A engages the nucleosome surface to aid chromatin recruitment.
Journal, issue, pagesEMBO Rep, Vol. 25, Issue 12, Page 5743-5779, Year 2024
Publish dateNov 11, 2024
AuthorsHannah Wapenaar / Gillian Clifford / Willow Rolls / Moira Pasquier / Hayden Burdett / Yujie Zhang / Gauri Deák / Juan Zou / Christos Spanos / Mark R D Taylor / Jacquie Mills / James A Watson / Dhananjay Kumar / Richard Clark / Alakta Das / Devisree Valsakumar / Janice Bramham / Philipp Voigt / Duncan Sproul / Marcus D Wilson /
PubMed AbstractDNA methyltransferase 3A (DNMT3A) plays a critical role in establishing and maintaining DNA methylation patterns in vertebrates. Here we structurally and biochemically explore the interaction of ...DNA methyltransferase 3A (DNMT3A) plays a critical role in establishing and maintaining DNA methylation patterns in vertebrates. Here we structurally and biochemically explore the interaction of DNMT3A1 with diverse modified nucleosomes indicative of different chromatin environments. A cryo-EM structure of the full-length DNMT3A1-DNMT3L complex with a H2AK119ub nucleosome reveals that the DNMT3A1 ubiquitin-dependent recruitment (UDR) motif interacts specifically with H2AK119ub and makes extensive contacts with the core nucleosome histone surface. This interaction facilitates robust DNMT3A1 binding to nucleosomes, and previously unexplained DNMT3A disease-associated mutations disrupt this interface. Furthermore, the UDR-nucleosome interaction synergises with other DNMT3A chromatin reading elements in the absence of histone ubiquitylation. H2AK119ub does not stimulate DNMT3A DNA methylation activity, as observed for the previously described H3K36me2 mark, which may explain low levels of DNA methylation on H2AK119ub marked facultative heterochromatin. This study highlights the importance of multivalent binding of DNMT3A to histone modifications and the nucleosome surface and increases our understanding of how DNMT3A1 chromatin recruitment occurs.
External linksEMBO Rep / PubMed:39528729 / PubMed Central
MethodsEM (single particle)
Resolution3.1 - 5.1 Å
Structure data

18778

8qzm

EMDB-18778, PDB-8qzm:
Structure of DNMT3A1 UDR region bound to H2AK119ub nucleosome
Method: EM (single particle) / Resolution: 3.1 Å

EMDB-18793: Cryo-EM density map of DNMT3A1-DNMT3L on a human H2AKc119ub nucleosome at 5.1 A resolution
Method: EM (single particle) / Resolution: 5.1 Å

Source
  • homo sapiens (human)
  • synthetic construct (others)
KeywordsDNA BINDING PROTEIN / Chromatin / Nucleosome / methyltransferase / Ubiquitin

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