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Structure paper

TitleThe +1 nucleosome functions in RNA Pol II transcription initiation and the transition to elongation.
Journal, issue, pagesMol Cell, Year 2026
Publish dateJul 21, 2026
AuthorsYumeng Zhan / Julio Abril-Garrido / Frauke Grabbe / Paulina Seweryn / Ute Neef / Christian Dienemann / Patrick Cramer /
PubMed AbstractTranscription initiation by RNA polymerase II (RNA Pol II) occurs next to a +1 nucleosome, which is positioned downstream of the transcription start site (TSS). The +1 nucleosome influences pre- ...Transcription initiation by RNA polymerase II (RNA Pol II) occurs next to a +1 nucleosome, which is positioned downstream of the transcription start site (TSS). The +1 nucleosome influences pre-initiation complex (PIC) assembly and RNA Pol II pausing, but its function in transcription initiation and the transition to elongation remains unclear. Here, we investigate the transcription initiation-elongation transition in vitro using DNA templates containing a +1 nucleosome and present cryo-electron microscopy (cryo-EM) structures of five intermediate states. First, after PIC assembly, ATP binding to TFIIH enables the +1 nucleosome to evict TFIID from the PIC. Following DNA opening, the +1 nucleosome stimulates TFIIH translocase activity and initial RNA synthesis. Finally, after DNA bubble rewinding, the +1 nucleosome removes TFIIH from the early elongation complex for promoter escape. Our findings show that the +1 nucleosome not only acts passively in PIC assembly and RNA Pol II pausing but rather has active functions during the initiation-elongation transition of transcription.
External linksMol Cell / PubMed:42480520
MethodsEM (single particle)
Resolution3.9 - 8.5 Å
Structure data

57364

29tk

EMDB-57364, PDB-29tk:
RNA polymerase II elongation complex with the +1 nucleosome
Method: EM (single particle) / Resolution: 3.9 Å

57390

29vf

EMDB-57390, PDB-29vf:
RNA polymerase II initially transcribing complex with a 2-nt RNA and the +1 nucleosome
Method: EM (single particle) / Resolution: 7.5 Å

57401

29wd

EMDB-57401: RNA polymerase II pre-initiation complex bound to ADP-BeF3 in the presence of the +1 nucleosome
PDB-29wd: RNA polymerase II initially transcribing complex with a 2-nt RNA and the +1 nucleosome
Method: EM (single particle) / Resolution: 4.2 Å

57691

30ff

EMDB-57691, PDB-30ff:
TFIID-containing RNA polymerase II pre-initiation complex in the presence of the +1 nucleosome
Method: EM (single particle) / Resolution: 8.5 Å

57693

30fh

EMDB-57693, PDB-30fh:
RNA polymerase II initially transcribing complex with a 6-nt RNA and the +1 nucleosome
Method: EM (single particle) / Resolution: 7.6 Å

Chemicals

ChemComp-ZN:
Unknown entry

ChemComp-MG:
Unknown entry

ChemComp-SF4:
IRON/SULFUR CLUSTER

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

ChemComp-BEF:
BERYLLIUM TRIFLUORIDE ION

ChemComp-UNK:
UNKNOWN

ChemComp-2A1:
(2S)-2-aminopropan-1-ol

ChemComp-ALA:
ALANINE

Source
  • homo sapiens (human)
  • sus scrofa (pig)
  • xenopus laevis (African clawed frog)
  • unidentified adenovirus
  • synthetic construct (others)
KeywordsTRANSCRIPTION / RNA polymerase II / Mammalian PIC / +1 nucleosome / transcription initiation

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