Zhang Xiaojie, Zhao Dan, Xiong Xiaozhe, He Zhimin, Li Haitao
From the Ministry of Education Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084 and.
From the Ministry of Education Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084 and; the Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China.
J Biol Chem. 2016 Jun 10;291(24):12786-12798. doi: 10.1074/jbc.M116.721159. Epub 2016 Apr 22.
The decoding of histone post-translational modifications by chromatin-binding modules ("readers") constitutes one major mechanism of epigenetic regulation. Nuclear antigen Sp100 (SPECKLED, 100 kDa), a constitutive component of the promyelocytic leukemia nuclear bodies, plays key roles in intrinsic immunity and transcriptional repression. Sp100C, a splicing isoform specifically up-regulated upon interferon stimulation, harbors a unique tandem plant homeodomain (PHD) finger and bromodomain at its C terminus. Combining structural, quantitative binding, and cellular co-localization studies, we characterized Sp100C PHD finger as an unmethylated histone H3 Lys(4) (H3K4me0) reader that tolerates histone H3 Thr(3) phosphorylation (H3T3ph), histone H3 Lys(9) trimethylation (H3K9me3), and histone H3 Ser(10) phosphorylation (H3S10ph), hallmarks associated with the mitotic chromosome. In contrast, whereas H3K4me0 reader activity is conserved in Sp140, an Sp100C paralog, the multivalent tolerance of H3T3ph, H3K9me3, and H3S10ph was lost for Sp140. The complex structure determined at 2.1 Å revealed a highly coordinated lysine ϵ-amine recognition sphere formed by an extended N-terminal motif for H3K4me0 readout. Interestingly, reader pocket rigidification by disulfide bond formation enhanced H3K4me0 binding by Sp100C. An additional complex structure solved at 2.7 Å revealed that H3T3ph is recognized by the arginine residue, Arg(713), that is unique to the PHD finger of Sp100C. Consistent with a restrictive cellular role of Sp100C, these results establish a direct chromatin targeting function of Sp100C that may regulate transcriptional gene silencing and promyelocytic leukemia nuclear body-mediated intrinsic immunity in response to interferon stimulation.
染色质结合模块（“读取器”）对组蛋白翻译后修饰的解码构成了表观遗传调控的一种主要机制。核抗原Sp100（斑点状，100 kDa）是早幼粒细胞白血病核体的组成成分，在固有免疫和转录抑制中起关键作用。Sp100C是一种在干扰素刺激后特异性上调的剪接异构体，在其C末端含有独特的串联植物同源结构域（PHD）指和溴结构域。结合结构、定量结合和细胞共定位研究，我们将Sp100C PHD指鉴定为未甲基化组蛋白H3赖氨酸（4）（H3K4me0）读取器，它可耐受组蛋白H3苏氨酸（3）磷酸化（H3T3ph）、组蛋白H3赖氨酸（9）三甲基化（H3K9me3）和组蛋白H3丝氨酸（10）磷酸化（H3S10ph），这些是与有丝分裂染色体相关的标志。相比之下，虽然H3K4me0读取器活性在Sp100C的旁系同源物Sp140中保守，但Sp140失去了对H3T3ph、H3K9me3和H3S10ph的多价耐受性。在2.1 Å分辨率下确定的复杂结构揭示了一个由用于H3K4me0读出的延伸N端基序形成的高度协调的赖氨酸ε-胺识别球。有趣的是，通过二硫键形成使读取器口袋刚性化增强了Sp100C对H3K4me0的结合。在2.7 Å分辨率下解析的另一个复杂结构表明，H3T3ph由Sp100C的PHD指特有的精氨酸残基Arg（713）识别。与Sp100C在细胞中的限制性作用一致，这些结果确立了Sp100C的直接染色质靶向功能，其可能在干扰素刺激下调节转录基因沉默和早幼粒细胞白血病核体介导的固有免疫。
