8JL9

Cryo-EM structure of the human nucleosome with scFv

Summary for 8JL9

• Entry DOI: 10.2210/pdb8jl9/pdb
• EMDB information: 36389
• Descriptor: Histone H3.1, Histone H4, Histone H2A type 1-B/E, ... (6 entities in total)
• Functional Keywords: nuclear protein, chromatin, gene regulation-dna complex, gene regulation/dna
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 10
• Total formula weight: 231293.93

Authors

Oishi, T.,Hatazawa, S.,Kujirai, T.,Kato, J.,Kobayashi, Y.,Ogasawara, M.,Akatsu, M.,Takizawa, Y.,Kurumizaka, H. (deposition date: 2023-06-02, release date: 2023-10-04, Last modification date: 2023-11-08)

Primary citation

Oishi, T.,Hatazawa, S.,Kujirai, T.,Kato, J.,Kobayashi, Y.,Ogasawara, M.,Akatsu, M.,Ehara, H.,Sekine, S.I.,Hayashi, G.,Takizawa, Y.,Kurumizaka, H.
Contributions of histone tail clipping and acetylation in nucleosome transcription by RNA polymerase II.
Nucleic Acids Res., 51:10364-10374, 2023

PubMed Abstract: The N-terminal tails of histones protrude from the nucleosome core and are target sites for histone modifications, such as acetylation and methylation. Histone acetylation is considered to enhance transcription in chromatin. However, the contribution of the histone N-terminal tail to the nucleosome transcription by RNA polymerase II (RNAPII) has not been clarified. In the present study, we reconstituted nucleosomes lacking the N-terminal tail of each histone, H2A, H2B, H3 or H4, and performed RNAPII transcription assays. We found that the N-terminal tail of H3, but not H2A, H2B and H4, functions in RNAPII pausing at the SHL(-5) position of the nucleosome. Consistently, the RNAPII transcription assay also revealed that the nucleosome containing N-terminally acetylated H3 drastically alleviates RNAPII pausing at the SHL(-5) position. In addition, the H3 acetylated nucleosome produced increased amounts of the run-off transcript. These results provide important evidence that the H3 N-terminal tail plays a role in RNAPII pausing at the SHL(-5) position of the nucleosome, and its acetylation directly alleviates this nucleosome barrier.

PubMed: 37718728
DOI: 10.1093/nar/gkad754

Experimental method

ELECTRON MICROSCOPY (2.65 Å)