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TitleStructural insights into how DEK nucleosome binding facilitates H3K27 trimethylation in chromatin.
Journal, issue, pagesNat Struct Mol Biol, Vol. 32, Issue 7, Page 1183-1192, Year 2025
Publish dateFeb 21, 2025
AuthorsTomoya Kujirai / Kenta Echigoya / Yusuke Kishi / Mai Saeki / Tomoko Ito / Junko Kato / Lumi Negishi / Hiroshi Kimura / Hiroshi Masumoto / Yoshimasa Takizawa / Yukiko Gotoh / Hitoshi Kurumizaka /
PubMed AbstractStructural diversity of the nucleosome affects chromatin conformations and regulates eukaryotic genome functions. Here we identify DEK, whose function is unknown, as a nucleosome-binding protein. In ...Structural diversity of the nucleosome affects chromatin conformations and regulates eukaryotic genome functions. Here we identify DEK, whose function is unknown, as a nucleosome-binding protein. In embryonic neural progenitor cells, DEK colocalizes with H3 K27 trimethylation (H3K27me3), the facultative heterochromatin mark. DEK stimulates the methyltransferase activity of Polycomb repressive complex 2 (PRC2), which is responsible for H3K27me3 deposition in vitro. Cryo-electron microscopy structures of the DEK-nucleosome complexes reveal that DEK binds the nucleosome by its tripartite DNA-binding mode on the dyad and linker DNAs and interacts with the nucleosomal acidic patch by its newly identified histone-binding region. The DEK-nucleosome interaction mediates linker DNA reorientation and induces chromatin compaction, which may facilitate PRC2 activation. These findings provide mechanistic insights into chromatin structure-mediated gene regulation by DEK.
External linksNat Struct Mol Biol / PubMed:39984731 / PubMed Central
MethodsEM (single particle)
Resolution2.8 - 4.0 Å
Structure data

37115

8kcy

EMDB-37115, PDB-8kcy:
Structure of nucleosome complexed with two DEK molecules
Method: EM (single particle) / Resolution: 2.8 Å

37121

8kd1

EMDB-37121, PDB-8kd1:
Structure of nucleosome complexed with one DEK molecule
Method: EM (single particle) / Resolution: 3.2 Å

37149

8ke0

EMDB-37149, PDB-8ke0:
Structure of H1.2 bound to the nucleosome
Method: EM (single particle) / Resolution: 4.0 Å

EMDB-38443: 193 bp Widom601L nucleosome (closed)
Method: EM (single particle) / Resolution: 3.4 Å

EMDB-38444: 193 bp Widom601L nucleosome (middle)
Method: EM (single particle) / Resolution: 3.7 Å

EMDB-38445: 193 bp Widom601L nucleosome (open)
Method: EM (single particle) / Resolution: 3.9 Å

Source
  • homo sapiens (human)
  • synthetic construct (others)
KeywordsDNA BINDING PROTEIN / Nucleosome / Chromatin / DNA / DEK / Complex / H1.2

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