Epigenetic regulation of gene expression occurs in a cell type-specific manner. Current cell-type specific neuroepigenetic studies rely on cell sorting methods that can alter cell phenotype and introduce potential confounds. Here we demonstrate and validate a Nuclear Tagging and Translating Ribosome Affinity Purification (NuTRAP) approach for temporally controlled labeling and isolation of ribosomes and nuclei, and thus RNA and DNA, from specific central nervous system cell types. Analysis of gene expression and DNA modifications in astrocytes or microglia from the same animal demonstrates differential usage of DNA methylation and hydroxymethylation in CpG and non-CpG contexts that corresponds to cell type-specific gene expression. Application of this approach in LPS treated mice uncovers microglia-specific transcriptome and epigenome changes in inflammatory pathways that cannot be detected with tissue-level analysis. The NuTRAP model and the validation approaches presented can be applied to any brain cell type for which a cell type-specific cre is available.

基因表达的表观遗传调控以细胞类型特异性方式发生。当前的细胞类型特异性神经表观遗传研究依赖于可以改变细胞表型并引入潜在混淆的细胞分选方法。在这里，我们演示并验证了核标签和翻译核糖体亲和纯化（NuTRAP）方法，用于从特定的中枢神经系统细胞类型中暂时控制核糖体和细胞核以及RNA和DNA的时间控制标记和分离。对同一动物的星形胶质细胞或小胶质细胞中基因表达和DNA修饰的分析表明，在CpG和非CpG情况下，对应于细胞类型特异性基因表达的DNA甲基化和羟甲基化的用法不同。该方法在LPS处理的小鼠中的应用揭示了小胶质细胞特异性转录组和表观基因组在炎症途径中的变化，而组织水平分析无法检测到这种变化。所提供的NuTRAP模型和验证方法可以应用于任何具有特定细胞类型cre的脑细胞类型。