Multiple structures of RNA polymerase II isolated from human nuclei by ChIP-CryoEM analysis

Tomoya Kujirai, Junko Kato, Kyoka Yamamoto, Seiya Hirai, Takeru Fujii, Kazumitsu Maehara, Akihito Harada, Lumi Negishi, Mitsuo Ogasawara, Yuki Yamaguchi, Yasuyuki Ohkawa, Yoshimasa Takizawa and Hitoshi Kurumizaka ()
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Tomoya Kujirai: 1-1-1 Yayoi
Junko Kato: 1-1-1 Yayoi
Kyoka Yamamoto: 1-1-1 Yayoi
Seiya Hirai: 1-1-1 Yayoi
Takeru Fujii: 3-1-1 Maidashi
Kazumitsu Maehara: 3-1-1 Maidashi
Akihito Harada: 3-1-1 Maidashi
Lumi Negishi: 1-1-1 Yayoi
Mitsuo Ogasawara: 1-1-1 Yayoi
Yuki Yamaguchi: 4259 Nagatsuta
Yasuyuki Ohkawa: 3-1-1 Maidashi
Yoshimasa Takizawa: 1-1-1 Yayoi
Hitoshi Kurumizaka: 1-1-1 Yayoi

Nature Communications, 2025, vol. 16, issue 1, 1-12

Abstract: Abstract 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.

Date: 2025
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DOI: 10.1038/s41467-025-59580-x

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