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. 2023 Sep 7;83(17):3080-3094.e14.
doi: 10.1016/j.molcel.2023.08.001. Epub 2023 Aug 25.

Mechanistic insights into nucleosomal H2B monoubiquitylation mediated by yeast Bre1-Rad6 and its human homolog RNF20/RNF40-hRAD6A

Zhiheng Deng  1 , Huasong Ai  2 , Maoshen Sun  1 , Zebin Tong  1 , Yunxiang Du  1 , Qian Qu  3 , Liying Zhang  1 , Ziyu Xu  1 , Shixian Tao  1 , Qiang Shi  1 , Jia-Bin Li  4 , Man Pan  3 , Lei Liu  5
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Mechanistic insights into nucleosomal H2B monoubiquitylation mediated by yeast Bre1-Rad6 and its human homolog RNF20/RNF40-hRAD6A

Zhiheng Deng et al. Mol Cell. .
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Abstract

Histone H2B monoubiquitylation plays essential roles in chromatin-based transcriptional processes. A RING-type E3 ligase (yeast Bre1 or human RNF20/RNF40) and an E2 ubiquitin-conjugating enzyme (yeast Rad6 or human hRAD6A), together, precisely deposit ubiquitin on H2B K123 in yeast or K120 in humans. Here, we developed a chemical trapping strategy and successfully captured the transient structures of Bre1- or RNF20/RNF40-mediated ubiquitin transfer from Rad6 or hRAD6A to nucleosomal H2B. Our structures show that Bre1 and RNF40 directly bind nucleosomal DNA, exhibiting a conserved E3/E2/nucleosome interaction pattern from yeast to humans for H2B monoubiquitylation. We also find an uncanonical non-hydrophobic contact in the Bre1 RING-Rad6 interface, which positions Rad6 directly above the target H2B lysine residue. Our study provides mechanistic insights into the site-specific monoubiquitylation of H2B, reveals a critical role of nucleosomal DNA in mediating E3 ligase recognition, and provides a framework for understanding the cancer-driving mutations of RNF20/RNF40.

Keywords: Bre1-Rad6; RNF20/RNF40-hRAD6A; chemical biology; cryo-electron microscopy; epigenetics; histone H2B monoubiquitylation; structural biology; ubiquitylation mechanism.

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Conflict of interest statement

Declaration of interests The authors declare no competing interests.

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