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TitleMultiple structures of RNA polymerase II isolated from human nuclei by ChIP-CryoEM analysis.
Journal, issue, pagesNat Commun, Vol. 16, Issue 1, Page 4724, Year 2025
Publish dateMay 28, 2025
AuthorsTomoya Kujirai / Junko Kato / Kyoka Yamamoto / Seiya Hirai / Takeru Fujii / Kazumitsu Maehara / Akihito Harada / Lumi Negishi / Mitsuo Ogasawara / Yuki Yamaguchi / Yasuyuki Ohkawa / Yoshimasa Takizawa / Hitoshi Kurumizaka /
PubMed AbstractRNA polymerase II (RNAPII) is a central transcription enzyme that exists as multiple forms with or without accessory factors, and transcribes the genomic DNA packaged in chromatin. To understand how ...RNA polymerase II (RNAPII) is a central transcription enzyme that exists as multiple forms with or without accessory factors, and transcribes the genomic DNA packaged in chromatin. To understand how RNAPII functions in the human genome, we isolate transcribing RNAPII complexes from human nuclei by chromatin immunopurification, and determine the cryo-electron microscopy structures of RNAPII elongation complexes (ECs) associated with genomic DNA in distinct forms, without or with the elongation factors SPT4/5, ELOF1, and SPT6. This ChIP-cryoEM method also reveals the two EC-nucleosome complexes corresponding nucleosome disassembly/reassembly processes. In the structure of EC-downstream nucleosome, EC paused at superhelical location (SHL) -5 in the nucleosome, suggesting that SHL(-5) pausing occurs in a sequence-independent manner during nucleosome disassembly. In the structure of the EC-upstream nucleosome, EC directly contacts the nucleosome through the nucleosomal DNA-RPB4/7 stalk and the H2A-H2B dimer-RPB2 wall interactions, suggesting that EC may be paused during nucleosome reassembly. These representative EC structures transcribing the human genome provide mechanistic insights into understanding RNAPII transcription on chromatin.
External linksNat Commun / PubMed:40436841 / PubMed Central
MethodsEM (single particle)
Resolution2.7 - 4.1 Å
Structure data

38604

8xrj

EMDB-38604, PDB-8xrj:
RNA polymerase II elongation complex with upstream nucleosome extracted from human nuclei
Method: EM (single particle) / Resolution: 3.6 Å

38607

8xrm

EMDB-38607, PDB-8xrm:
RNA polymerase II elongation complex with DSIF, SPT6, and ELOF1 transcribing genomic DNA extracted from human nuclei
Method: EM (single particle) / Resolution: 3.13 Å

38624

8xso

EMDB-38624, PDB-8xso:
RNA polymerase II elongation complex transcribing genomic DNA extracted from human nuclei
Method: EM (single particle) / Resolution: 2.7 Å

38717

8xvs

EMDB-38717, PDB-8xvs:
RNA polymerase II elongation complex with downstream nucleosome extracted from human nuclei
Method: EM (single particle) / Resolution: 4.1 Å

Chemicals

ChemComp-ZN:
Unknown entry

ChemComp-MG:
Unknown entry

Source
  • homo sapiens (human)
KeywordsTRANSCRIPTION/DNA/RNA / nucleus / nucleosome / TRANSCRIPTION-DNA-RNA COMPLEX / TRANSCRIPTION/RNA/DNA / TRANSCRIPTION-RNA-DNA COMPLEX / complex / RNA polymerase

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