Structural basis of the crosstalk between histone H2B monoubiquitination and H3 lysine 79 methylation on nucleosome
Structural basis of the crosstalk between histone H2B monoubiquitination and H3 lysine 79 methylation on nucleosome
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DOI：
10.1038/s41422-019-0146-7
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发表时间：
2019-02
期刊：
影响因子：
44.1
通讯作者：
Tonghui Yao;Wei Jing;Zhiguo Hu;Ming-Dian Tan;Mi Cao;Qianmin Wang;Yan Li;Guiyong Yuan;M. Lei;Jing Huang
中科院分区：
文献类型：
--
作者：
Tonghui Yao;Wei Jing;Zhiguo Hu;Ming-Dian Tan;Mi Cao;Qianmin Wang;Yan Li;Guiyong Yuan;M. Lei;Jing Huang
尊敬的编辑，翻译后修饰（PTM）沉积的组蛋白标记经常以相互关联的组合模式出现，以创建对染色质结构和功能的复杂而精确的控制。1组蛋白PTM串扰的标志性发现之一是通过组蛋白H2 B在赖氨酸120（H2 BK 120）上的单泛素化对组蛋白H3赖氨酸79（H3 K79）甲基化的跨组蛋白调节。2组蛋白H3 K79的单甲基化、双甲基化和三甲基化是一种重要的组蛋白标记，参与转录调控和DNA损伤反应。3 H2 BK 120单泛素化（H2 BK 120 ub 1）是独特的非SET结构域的组蛋白甲基转移酶DOT 1 L（Disrupter of telomere silencing protein 1-like）在体内有效甲基化H3 K79的先决条件。2将化学单泛素化的H2 B掺入体外重构的核小体中直接刺激DOT 1 L 4的催化活性（补充信息，图1A和1B）。S1和S2）。H3 K79甲基标记如何沉积以及相关的PTM串扰如何发生在核小体上仍然知之甚少。在这里，我们以4.1 μ m的总分辨率呈现了与H2 BK 120 ub 1核小体核心颗粒（缩写为ubNCP）复合的人DOT 1 L的催化结构域（残基1-416）的冷冻电子显微镜（cryo-EM）结构（补充信息，图1A和1B）。S3-S5和表S1）。DOT 1 L-ubNCP的结构揭示了DOT 1 L广泛地与核小体盘面上的核心组蛋白相互作用（掩埋表面积，~ 2020 μ 2），其C末端区域（残基269-331）夹在泛素和组蛋白H2 A-H2 B二聚体之间（图1a）。DOT 1 L与H2 BK 120结合的泛素的直接结合扩展了DOT 1 L与组蛋白表面之间的识别界面，并可能增加了DOT 1 L与H2 BK 120 ub 1核小体的结合亲和力。我们使用了DOT 1 L构建体（残基1-351），它缺乏一个带正电荷的区域，结合核小体DNA，比较其结合亲和力的组蛋白表面的NCP和ubNCP。GST-下拉测定清楚地显示DOT 1 L1 -351仅与泛素化的核小体相互作用，表明H2 BK 120 ub 1显著增加DOT 1 L与核小体的组蛋白表面的弱缔合（补充信息，图S6 b，泳道7-9）。对H2 BK 120 ub 1核小体的结合亲和力增加导致DOT 1 L的催化效率增强以及更高水平的H3 K79二甲基化和三甲基化的积累（补充信息，图S2）。我们还确定了DOT 1 L与未修饰的NCP复合物的冷冻-EM结构，总分辨率为5.0 nm（补充信息，图S7和表S1）。这种3D重建中的DOT 1 L密度不够清晰，无法建立原子模型。然而，DOT 1 L-ubNCP复合物结构对接到该图中显示DOT 1 L-ubNCP结构与DOT 1 L-NCP密度图的良好拟合，表明
Dear Editor, Histone marks deposited by post-translational modifications (PTMs) frequently occur in interrelated combinational patterns to create a complex and precise control on the chromatin structure and function. 1 One of the landmark findings of histone PTM crosstalk is the trans-histone regulation of histone H3 lysine 79 (H3K79) methylation by the monoubiquitination of histone H2B on lysine 120 (H2BK120). 2 Mono-, di-, and tri-methylation of histone H3K79 serves as a prominent histone mark that participates in transcription regulation and DNA damage response. 3 H2BK120 monoubiquitination (H2BK120ub1) is a prerequisite for the efficient methylation of H3K79 by the unique non-SET domaincontaining histone methyltransferase DOT1L (Disrupter of telomere silencing protein 1-like) in vivo. 2 Incorporation of chemically monoubiquitinated H2B into in vitro reconstituted nucleosome directly stimulates the catalytic activity of DOT1L 4 (Supplementary information, Figs. S1 and S2). It still remains poorly understood how the H3K79 methyl marks are deposited and how the associated PTM crosstalk occurs on nucleosome. Here we present the cryo-electron microscopy (cryo-EM) structure of the catalytic domain of human DOT1L (residues 1-416) in complex with an H2BK120ub1 nucleosome core particle (abbreviated as ubNCP) at an overall resolution of 4.1 Å (Supplementary information, Figs. S3-S5 and Table S1). The structure of DOT1L-ubNCP reveals that DOT1L extensively interacts with core histones on the disk-face of nucleosome (buried surface area,~ 2020 Å2), with its C-terminal region (residues 269-331) sandwiched between ubiquitin and the histone H2A-H2B dimer (Fig. 1 a). The direct association of DOT1L with the H2BK120-conjugated ubiquitin extends the recognition interface between DOT1L and histone surface, and probably increases the binding affinity of DOT1L toward the H2BK120ub1 nucleosome. We used a DOT1L construct (residues 1-351), which lacks a positively charged region that binds the nucleosomal DNA, to compare its binding affinity to the histone surface of NCP and ubNCP. GST-pull-down assay clearly showed that DOT1L1-351 only interacts with the ubiquitinated nucleosome, indicating that H2BK120ub1 dramatically increases the weak association of DOT1L with the histone surface of nucleosome (Supplementary information, Fig. S6b, lanes 7-9). The increased binding affinity toward the H2BK120ub1 nucleosome results in the enhanced catalytic efficiency of DOT1L and the accumulation of higher levels of H3K79 di-and tri-methylation (Supplementary information, Fig. S2).We also determined the cryo-EM structure of DOT1L in complex with an unmodified NCP at an overall resolution of 5.0 Å (Supplementary information, Fig. S7 and Table S1). The density of DOT1L in this 3D reconstruction is not clear enough to build an atomic model. However, docking of the DOT1L-ubNCP complex structure into this map shows a good fit of the DOT1L-ubNCP structure with the DOT1L-NCP density map, indicating that