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Structure paper

TitleStructural insights into promoter-proximal pausing of RNA polymerase II at +1 nucleosome.
Journal, issue, pagesSci Adv, Vol. 11, Issue 10, Page eadu0577, Year 2025
Publish dateMar 7, 2025
AuthorsMasahiro Naganuma / Tomoya Kujirai / Haruhiko Ehara / Tamami Uejima / Tomoko Ito / Mie Goto / Mari Aoki / Masami Henmi / Sayako Miyamoto-Kohno / Mikako Shirouzu / Hitoshi Kurumizaka / Shun-Ichi Sekine /
PubMed AbstractThe metazoan transcription elongation complex (EC) of RNA polymerase II (RNAPII) generally stalls between the transcription start site and the first (+1) nucleosome. This promoter-proximal pausing ...The metazoan transcription elongation complex (EC) of RNA polymerase II (RNAPII) generally stalls between the transcription start site and the first (+1) nucleosome. This promoter-proximal pausing involves negative elongation factor (NELF), 5,6-dichloro-1-β-d-ribobenzimidazole sensitivity-inducing factor (DSIF), and transcription elongation factor IIS (TFIIS) and is critical for subsequent productive transcription elongation. However, the detailed pausing mechanism and the involvement of the +1 nucleosome remain enigmatic. Here, we report cryo-electron microscopy structures of ECs stalled on nucleosomal DNA. In the absence of TFIIS, the EC is backtracked/arrested due to conflicts between NELF and the nucleosome. We identified two alternative binding modes of NELF, one of which reveals a critical contact with the downstream DNA through the conserved NELF-E basic helix. Upon binding with TFIIS, the EC progressed to the nucleosome to establish a paused EC with a partially unwrapped nucleosome. This paused EC strongly restricts EC progression further downstream. These structures illuminate the mechanism of RNAPII pausing/stalling at the +1 nucleosome.
External linksSci Adv / PubMed:40043114 / PubMed Central
MethodsEM (single particle)
Resolution3.3 - 3.4 Å
Structure data

61058

9j0n

EMDB-61058, PDB-9j0n:
Paused elongation complex of mammalian RNA polymerase II with nucleosome (PEC2-nuc)
Method: EM (single particle) / Resolution: 3.4 Å

61059

9j0o

EMDB-61059, PDB-9j0o:
Arrested elongation complex of mammalian RNA polymerase II with nucleosome (AEC1-nuc)
Method: EM (single particle) / Resolution: 3.3 Å

61060

9j0p

EMDB-61060, PDB-9j0p:
Arrested elongation complex of mammalian RNA polymerase II with nucleosome (AEC2-nuc)
Method: EM (single particle) / Resolution: 3.3 Å

Chemicals

ChemComp-ZN:
Unknown entry

ChemComp-MG:
Unknown entry

Source
  • sus scrofa (pig)
  • homo sapiens (human)
KeywordsTRANSCRIPTION / RNA polymerase / NELF / nucleosome / DNA / RNA / TFIIS

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