Epigenetic regulators have a crucial effect on gene expression based on their manipulation of histone modifications. Histone H2AK119 monoubiquitination (H2AK119Ub), a well-established hallmark in transcription repression, is dynamically regulated by the opposing activities of Polycomb repressive complex 1 (PRC1) and nucleosome deubiquitinases including the primary human USP16 and Polycomb repressive deubiquitinase (PR-DUB) complex. Recently, the catalytic mechanism for the multi-subunit PR-DUB complex has been described, but how the single-subunit USP16 recognizes the H2AK119Ub nucleosome and cleaves the ubiquitin (Ub) remains unknown. Here we report the cryo-EM structure of USP16–H2AK119Ub nucleosome complex, which unveils a fundamentally distinct mode of H2AK119Ub deubiquitination compared to PR-DUB, encompassing the nucleosome recognition pattern independent of the H2A–H2B acidic patch and the conformational heterogeneity in the Ub motif and the histone H2A C-terminal tail. Our work highlights the mechanism diversity of H2AK119Ub deubiquitination and provides a structural framework for understanding the disease-causing mutations of USP16.

表观遗传调节因子基于它们对组蛋白修饰的操纵，对基因表达具有至关重要的影响。组蛋白H2AK119单泛素化 （H2AK119Ub） 是转录抑制中公认的标志，受多梳抑制复合物 1 （PRC1） 和核小体去泛素酶（包括原代人 USP16 和多梳抑制性去泛素酶 （PR-DUB） 复合物）的相反活性动态调节。最近，已经描述了多亚基 PR-DUB 复合物的催化机制，但单亚基 USP16 如何识别 H2AK119Ub 核小体并裂解泛素 （Ub） 仍然未知。在这里，我们报道了 USP16-H2AK119Ub 核小体复合物的冷冻电镜结构，与 PR-DUB 相比，它揭示了 H2AK119Ub 去泛素化的根本不同模式，包括独立于 H2A-H2B 酸性贴片的核小体识别模式以及 Ub 基序和组蛋白 H2A C 末端尾部的构象异质性。我们的工作突出了 H2AK119Ub 去泛素化的机制多样性，并为理解 USP16 的致病突变提供了结构框架。