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TitleStructural basis of RNAPII transcription on the nucleosome containing histone variant H2A.B.
Journal, issue, pagesEMBO J, Vol. 44, Issue 14, Page 4065-4087, Year 2025
Publish dateMay 30, 2025
AuthorsMunetaka Akatsu / Rina Hirano / Tomoya Kujirai / Mitsuo Ogasawara / Haruhiko Ehara / Shun-Ichi Sekine / Yoshimasa Takizawa / Hitoshi Kurumizaka /
PubMed AbstractH2A.B is a distant histone H2A variant associated with actively transcribed regions of the genome, suggesting its positive role in promoting transcription. In the present study, we demonstrate that ...H2A.B is a distant histone H2A variant associated with actively transcribed regions of the genome, suggesting its positive role in promoting transcription. In the present study, we demonstrate that the RNA polymerase II elongation complex (EC) transcribes the nucleosome containing H2A.B more efficiently than that with canonical H2A in vitro. Our cryo-electron microscopy analysis of the H2A.B nucleosome during transcription revealed that the proximal H2A.B-H2B dimer is released from the nucleosome as the EC transcribes the proximal half of the nucleosomal DNA. This dissociation, which is not observed in the canonical H2A nucleosome, likely enhances the EC elongation efficiency in the H2A.B nucleosome. Mutational analyses suggested that the unique short C-terminal region of H2A.B alone enhances EC elongation efficiency when substituted for its counterpart in canonical H2A. Additionally, other regions of H2A.B contribute to this enhancement. These structural and biochemical findings provide new insights into the role of H2A.B in regulating gene expression.
External linksEMBO J / PubMed:40447801 / PubMed Central
MethodsEM (single particle)
Resolution3.5 - 4.7 Å
Structure data

EMDB-60592: RNA polymerase II elongation complex stalled at SHL(-5) of the nucleosome containing histone variant H2A.B
Method: EM (single particle) / Resolution: 4.7 Å

60593

9ii7

EMDB-60593, PDB-9ii7:
RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome containing histone variant H2A.B
Method: EM (single particle) / Resolution: 3.5 Å

Chemicals

ChemComp-ZN:
Unknown entry

ChemComp-MG:
Unknown entry

Source
  • komagataella phaffii (fungus)
  • homo sapiens (human)
  • synthetic construct (others)
KeywordsTRANSCRIPTION / Transcription-DNA-RNA COMPLEX / RNAPII

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