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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

0671

6j4w

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

0672

6j4x

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

0673

6j4y

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

0674

6j4z

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

0675

6j50

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

0676

6j51

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

9713

6ir9

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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