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TitleStructural Basis of Damaged Nucleotide Recognition by Transcribing RNA Polymerase II in the Nucleosome.
Journal, issue, pagesJ Mol Biol, Vol. 435, Issue 13, Page 168130, Year 2023
Publish dateJul 1, 2023
AuthorsKen Osumi / Tomoya Kujirai / Haruhiko Ehara / Mitsuo Ogasawara / Chiaki Kinoshita / Mika Saotome / Wataru Kagawa / Shun-Ichi Sekine / Yoshimasa Takizawa / Hitoshi Kurumizaka /
PubMed AbstractIn transcription-coupled repair (TCR), transcribing RNA polymerase II (RNAPII) stalls at a DNA lesion and recruits TCR proteins to the damaged site. However, the mechanism by which RNAPII recognizes ...In transcription-coupled repair (TCR), transcribing RNA polymerase II (RNAPII) stalls at a DNA lesion and recruits TCR proteins to the damaged site. However, the mechanism by which RNAPII recognizes a DNA lesion in the nucleosome remains enigmatic. In the present study, we inserted an apurinic/apyrimidinic DNA lesion analogue, tetrahydrofuran (THF), in the nucleosomal DNA, where RNAPII stalls at the SHL(-4), SHL(-3.5), and SHL(-3) positions, and determined the structures of these complexes by cryo-electron microscopy. In the RNAPII-nucleosome complex stalled at SHL(-3.5), the nucleosome orientation relative to RNAPII is quite different from those in the SHL(-4) and SHL(-3) complexes, which have nucleosome orientations similar to naturally paused RNAPII-nucleosome complexes. Furthermore, we found that an essential TCR protein, Rad26 (CSB), enhances the RNAPII processivity, and consequently augments the DNA damage recognition efficiency of RNAPII in the nucleosome. The cryo-EM structure of the Rad26-RNAPII-nucleosome complex revealed that Rad26 binds to the stalled RNAPII through a novel interface, which is completely different from those previously reported. These structures may provide important information to understand the mechanism by which RNAPII recognizes the nucleosomal DNA lesion and recruits TCR proteins to the stalled RNAPII on the nucleosome.
External linksJ Mol Biol / PubMed:37120012
MethodsEM (single particle)
Resolution4.0 - 7.1 Å
Structure data

32407

7wbv

EMDB-32407, PDB-7wbv:
RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-4) of the nucleosome
Method: EM (single particle) / Resolution: 4.1 Å

32408

7wbw

EMDB-32408, PDB-7wbw:
RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-3.5) of the nucleosome
Method: EM (single particle) / Resolution: 7.1 Å

32409

7wbx

EMDB-32409, PDB-7wbx:
RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-3) of the nucleosome
Method: EM (single particle) / Resolution: 4.0 Å

34685

8he5

EMDB-34685, PDB-8he5:
RNA polymerase II elongation complex bound with Rad26 and Elf1, stalled at SHL(-3.5) of the nucleosome
Method: EM (single particle) / Resolution: 6.95 Å

Chemicals

ChemComp-ZN:
Unknown entry

ChemComp-MG:
Unknown entry

Source
  • komagataella phaffii (fungus)
  • homo sapiens (human)
  • synthetic construct (others)
  • Komagataella pastoris (fungus)
KeywordsTRANSCRIPTION / RNA / DNA / Repair

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