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Structure paper

TitleStructural basis of the nucleosome transition during RNA polymerase II passage.
Journal, issue, pagesScience, Vol. 362, Issue 6414, Page 595-598, Year 2018
Publish dateNov 2, 2018
AuthorsTomoya Kujirai / Haruhiko Ehara / Yuka Fujino / Mikako Shirouzu / Shun-Ichi Sekine / Hitoshi Kurumizaka /
PubMed AbstractGenomic DNA forms chromatin, in which the nucleosome is the repeating unit. The mechanism by which RNA polymerase II (RNAPII) transcribes the nucleosomal DNA remains unclear. Here we report the cryo- ...Genomic DNA forms chromatin, in which the nucleosome is the repeating unit. The mechanism by which RNA polymerase II (RNAPII) transcribes the nucleosomal DNA remains unclear. Here we report the cryo-electron microscopy structures of RNAPII-nucleosome complexes in which RNAPII pauses at the superhelical locations SHL(-6), SHL(-5), SHL(-2), and SHL(-1) of the nucleosome. RNAPII pauses at the major histone-DNA contact sites, and the nucleosome interactions with the RNAPII subunits stabilize the pause. These structures reveal snapshots of nucleosomal transcription, in which RNAPII gradually tears DNA from the histone surface while preserving the histone octamer. The nucleosomes in the SHL(-1) complexes are bound to a "foreign" DNA segment, which might explain the histone transfer mechanism. These results provide the foundations for understanding chromatin transcription and epigenetic regulation.
External linksScience / PubMed:30287617
MethodsEM (single particle) / EM (electron crystallography)
Resolution5.6 - 9.9 Å
Structure data

6980

6a5l

EMDB-6980, PDB-6a5l:
RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA
Method: EM (single particle) / Resolution: 5.6 Å

6981

6a5o

EMDB-6981, PDB-6a5o:
RNA polymerase II elongation complex stalled at SHL(-6) of the nucleosome
Method: EM (single particle) / Resolution: 9.9 Å

6982

6a5p

EMDB-6982, PDB-6a5p:
RNA polymerase II elongation complex stalled at SHL(-5) of the nucleosome
Method: EM (single particle) / Resolution: 7.0 Å

6983

6a5r

EMDB-6983, PDB-6a5r:
RNA polymerase II elongation complex stalled at SHL(-2) of the nucleosome
Method: EM (single particle) / Resolution: 8.7 Å

6984

6a5t

EMDB-6984, PDB-6a5t:
RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome
Method: EM (single particle) / Resolution: 6.7 Å

6985

6a5u

EMDB-6985, PDB-6a5u:
RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA, tilt conformation
Method: EM (single particle) / Resolution: 7.6 Å

6986

6inq

EMDB-6986, PDB-6inq:
RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA (+1 position)
Method: EM (single particle) / Resolution: 6.9 Å

Chemicals

ChemComp-ZN:
Unknown entry

ChemComp-MG:
Unknown entry

Source
  • Komagataella phaffii (fungus)
  • komagataella phaffii (strain gs115 / atcc 20864) (fungus)
  • homo sapiens (human)
  • synthetic construct (others)
  • Yeast (fungus)
KeywordsTRANSCRIPTION/RNA/DNA / nucleosome / chromatin / RNA polymerase / TRANSCRIPTION / TRANSCRIPTION-RNA-DNA complex

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