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Structure paper

TitleStructural insight into nucleosome transcription by RNA polymerase II with elongation factors.
Journal, issue, pagesScience, Vol. 363, Issue 6428, Page 744-747, Year 2019
Publish dateFeb 15, 2019
AuthorsHaruhiko Ehara / Tomoya Kujirai / Yuka Fujino / Mikako Shirouzu / Hitoshi Kurumizaka / Shun-Ichi Sekine /
PubMed AbstractRNA polymerase II (RNAPII) transcribes chromosomal DNA that contains multiple nucleosomes. The nucleosome forms transcriptional barriers, and nucleosomal transcription requires several additional ...RNA polymerase II (RNAPII) transcribes chromosomal DNA that contains multiple nucleosomes. The nucleosome forms transcriptional barriers, and nucleosomal transcription requires several additional factors in vivo. We demonstrate that the transcription elongation factors Elf1 and Spt4/5 cooperatively lower the barriers and increase the RNAPII processivity in the nucleosome. The cryo-electron microscopy structures of the nucleosome-transcribing RNAPII elongation complexes (ECs) reveal that Elf1 and Spt4/5 reshape the EC downstream edge and intervene between RNAPII and the nucleosome. They facilitate RNAPII progression through superhelical location SHL(-1) by adjusting the nucleosome in favor of the forward progression. They suppress pausing at SHL(-5) by preventing the stable RNAPII-nucleosome interaction. Thus, the EC overcomes the nucleosomal barriers while providing a platform for various chromatin functions.
External linksScience / PubMed:30733384
MethodsEM (single particle)
Resolution3.8 - 7.9 Å
Structure data

EMDB-0671, PDB-6j4w:
RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-5) of the nucleosome
Method: EM (single particle) / Resolution: 7.9 Å

EMDB-0672, PDB-6j4x:
RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-1) of the nucleosome (+1A)
Method: EM (single particle) / Resolution: 4.3 Å

EMDB-0673, PDB-6j4y:
RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-1) of the nucleosome (+1B)
Method: EM (single particle) / Resolution: 4.3 Å

EMDB-0674, PDB-6j4z:
RNA polymerase II elongation complex bound with Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome
Method: EM (single particle) / Resolution: 4.1 Å

EMDB-0675, PDB-6j50:
RNA polymerase II elongation complex bound with Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome (tilted conformation)
Method: EM (single particle) / Resolution: 4.7 Å

EMDB-0676, PDB-6j51:
RNA polymerase II elongation complex bound with Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome, weak Elf1 (+1 position)
Method: EM (single particle) / Resolution: 4.2 Å

EMDB-9713, PDB-6ir9:
RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-1) of the nucleosome
Method: EM (single particle) / Resolution: 3.8 Å

Chemicals

ChemComp-ZN:
Unknown entry

ChemComp-MG:
Unknown entry

Source
  • komagataella pastoris (fungus)
  • komagataella phaffii (strain gs115 / atcc 20864) (fungus)
  • komagataella phaffii (strain atcc 76273 / cbs 7435 / cect 11047 / nrrl y-11430 / wegner 21-1) (fungus)
  • homo sapiens (human)
  • synthetic construct (others)
  • komagataella phaffii (fungus)
KeywordsTRANSCRIPTION/RNA/DNA / nucleosome / chromatin / RNA polymerase / TRANSCRIPTION / TRANSCRIPTION-RNA-DNA complex

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