Joint single-cell profiling resolves 5mC and 5hmC and reveals their distinct gene regulatory effects.
Joint single-cell profiling resolves 5mC and 5hmC and reveals their distinct gene regulatory effects.
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联合单细胞分析解析了 5mC 和 5hmC，并揭示了它们独特的基因调控作用。
DOI：
10.1038/s41587-023-01909-2
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发表时间：
2023
影响因子：
46.9
通讯作者：
Wu,Hao
中科院分区：
文献类型：
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作者：
Fabyanic,EmilyB;Hu,Peng;Qiu,Qi;Berríos,KiaraN;Connolly,DanielR;Wang,Tong;Flournoy,Jennifer;Zhou,Zhaolan;Kohli,RahulM;Wu,Hao
10 - 11易位（泰特）DNA双加氧酶对5-甲基胞嘧啶（5 mC）的氧化修饰产生5-羟甲基胞嘧啶（5 hmC），其是氧化的5 mC的最丰富形式。现有的单细胞亚硫酸氢盐测序方法不能解析5 mC和5 hmC，使得泰特和5 hmC的细胞类型特异性调节机制在很大程度上未知。在这里，我们提出了联合单核（羟基）甲基胞嘧啶测序（Joint-snhmC-seq），这是一种可扩展的定量方法，通过利用APOBEC 3A对5 mC和化学保护的5 hmC的差异脱氨酶活性，同时在单细胞中分析5 hmC和真正的5 mC。来自小鼠脑的单个核的联合snhmC-seq分析揭示了在单细胞分辨率下5 hmC和真实5 mC的表观遗传异质性的前所未有的水平。我们发现，细胞类型特异性的5 hmC或真正的5 mC的配置文件，提高多模式的单细胞数据集成，使神经元亚型的准确识别，并揭示特定的上下文特定的调控效应细胞类型特异性基因的泰特酶。
Oxidative modification of 5-methylcytosine (5mC) by ten-eleven translocation (TET) DNA dioxygenases generates 5-hydroxymethylcytosine (5hmC), the most abundant form of oxidized 5mC. Existing single-cell bisulfite sequencing methods cannot resolve 5mC and 5hmC, leaving the cell-type-specific regulatory mechanisms of TET and 5hmC largely unknown. Here, we present joint single-nucleus (hydroxy)methylcytosine sequencing (Joint-snhmC-seq), a scalable and quantitative approach that simultaneously profiles 5hmC and true 5mC in single cells by harnessing differential deaminase activity of APOBEC3A toward 5mC and chemically protected 5hmC. Joint-snhmC-seq profiling of single nuclei from mouse brains reveals an unprecedented level of epigenetic heterogeneity of both 5hmC and true 5mC at single-cell resolution. We show that cell-type-specific profiles of 5hmC or true 5mC improve multimodal single-cell data integration, enable accurate identification of neuronal subtypes and uncover context-specific regulatory effects on cell-type-specific genes by TET enzymes.