EMD-36252
RNA polymerase II elongation complex containing 40 bp upstream DNA loop, stalled at SHL(-1) of the nucleosome
EMD-36252
Single-particle3.7 Å
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Map released: 29/11/2023
Last modified: 20/12/2023
Sample Organism:
Komagataella phaffii,
Homo sapiens,
synthetic construct
Sample: RNA polymerase II - nucleosome complex
Fitted models: 8jh3 (Avg. Q-score: 0.255)
Deposition Authors: Akatsu M
,
Fujita R,
Ogasawara M,
Ehara H
,
Kujirai T,
Takizawa Y,
Sekine S,
Kurumizaka H
Sample: RNA polymerase II - nucleosome complex
Fitted models: 8jh3 (Avg. Q-score: 0.255)
Deposition Authors: Akatsu M
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Cryo-EM structures of RNA polymerase II-nucleosome complexes rewrapping transcribed DNA.
Akatsu M
,
Ehara H
,
Kujirai T,
Fujita R,
Ito T,
Osumi K,
Ogasawara M,
Takizawa Y,
Sekine SI
,
Kurumizaka H
(2023) J Biol Chem , 299 , 105477 - 105477
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(2023) J Biol Chem , 299 , 105477 - 105477
Abstract:
RNA polymerase II (RNAPII) transcribes DNA wrapped in the nucleosome by stepwise pausing, especially at nucleosomal superhelical locations -5 and -1 [SHL(-5) and SHL(-1), respectively]. In the present study, we performed cryo-electron microscopy analyses of RNAPII-nucleosome complexes paused at a major nucleosomal pausing site, SHL(-1). We determined two previously undetected structures, in which the transcribed DNA behind RNAPII is sharply kinked at the RNAPII exit tunnel and rewrapped around the nucleosomal histones in front of RNAPII by DNA looping. This DNA kink shifts the DNA orientation toward the nucleosome, and the transcribed DNA region interacts with basic amino acid residues of histones H2A, H2B, and H3 exposed by the RNAPII-mediated nucleosomal DNA peeling. The DNA loop structure was not observed in the presence of the transcription elongation factors Spt4/5 and Elf1. These RNAPII-nucleosome structures provide important information for understanding the functional relevance of DNA looping during transcription elongation in the nucleosome.
RNA polymerase II (RNAPII) transcribes DNA wrapped in the nucleosome by stepwise pausing, especially at nucleosomal superhelical locations -5 and -1 [SHL(-5) and SHL(-1), respectively]. In the present study, we performed cryo-electron microscopy analyses of RNAPII-nucleosome complexes paused at a major nucleosomal pausing site, SHL(-1). We determined two previously undetected structures, in which the transcribed DNA behind RNAPII is sharply kinked at the RNAPII exit tunnel and rewrapped around the nucleosomal histones in front of RNAPII by DNA looping. This DNA kink shifts the DNA orientation toward the nucleosome, and the transcribed DNA region interacts with basic amino acid residues of histones H2A, H2B, and H3 exposed by the RNAPII-mediated nucleosomal DNA peeling. The DNA loop structure was not observed in the presence of the transcription elongation factors Spt4/5 and Elf1. These RNAPII-nucleosome structures provide important information for understanding the functional relevance of DNA looping during transcription elongation in the nucleosome.