Liu Yingying, Zhang Yanjun, Xue Han, Cao Mi, Bai Guohui, Mu Zongkai, Yao Yanli, Sun Shuyang, Fang Dong, Huang Jing
Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200125, China.
Shanghai Institute of Precision Medicine, Shanghai, 200125, China.
Cell Discov. 2021 May 11;7(1):32. doi: 10.1038/s41421-021-00261-6.
Substitution of lysine 36 with methionine in histone H3.3 (H3.3K36M) is an oncogenic mutation that inhibits SETD2-mediated histone H3K36 tri-methylation in tumors. To investigate how the oncohistone mutation affects the function of SETD2 at the nucleosome level, we determined the cryo-EM structure of human SETD2 associated with an H3.3K36M nucleosome and cofactor S-adenosylmethionine (SAM), and revealed that SETD2 is attached to the N-terminal region of histone H3 and the nucleosome DNA at superhelix location 1, accompanied with the partial unwrapping of nucleosome DNA to expose the SETD2-binding site. These structural features were also observed in the previous cryo-EM structure of the fungal Set2-nucleosome complex. By contrast with the stable association of SETD2 with the H3.3K36M nucleosome, the EM densities of SETD2 could not be observed on the wild-type nucleosome surface, suggesting that the association of SETD2 with wild-type nucleosome might be transient. The linker histone H1, which stabilizes the wrapping of nucleosome DNA at the entry/exit sites, exhibits an inhibitory effect on the activities of SETD2 and displays inversely correlated genome distributions with that of the H3K36me3 marks. Cryo-EM analysis of yeast H3K36 methyltransferase Set2 complexed with nucleosomes further revealed evolutionarily conserved structural features for nucleosome recognition in eukaryotes, and provides insights into the mechanism of activity regulation. These findings have advanced our understanding of the structural basis for the tumorigenesis mechanism of the H3.3K36M mutation and highlight the effect of nucleosome conformation on the regulation of histone modification.
组蛋白H3.3中赖氨酸36被甲硫氨酸取代（H3.3K36M）是一种致癌突变，可抑制肿瘤中SETD2介导的组蛋白H3K36三甲基化。为了研究这种致癌组蛋白突变如何在核小体水平上影响SETD2的功能，我们确定了与H3.3K36M核小体和辅因子S-腺苷甲硫氨酸（SAM）相关的人SETD2的冷冻电镜结构，并揭示SETD2附着于组蛋白H3的N端区域和超螺旋位置1处的核小体DNA，同时伴随着核小体DNA的部分解旋以暴露SETD2结合位点。这些结构特征也在先前真菌Set2-核小体复合物的冷冻电镜结构中观察到。与SETD2与H3.3K36M核小体的稳定结合相反，在野生型核小体表面未观察到SETD2的电镜密度，这表明SETD2与野生型核小体的结合可能是短暂的。连接组蛋白H1可稳定核小体DNA在进出位点的包裹，对SETD2的活性具有抑制作用，并且其在基因组中的分布与H3K36me3标记呈负相关。对与核小体复合的酵母H3K36甲基转移酶Set2的冷冻电镜分析进一步揭示了真核生物中核小体识别的进化保守结构特征，并为活性调节机制提供了见解。这些发现加深了我们对H3.3K36M突变致瘤机制结构基础的理解，并突出了核小体构象对组蛋白修饰调节的影响。
