Biotin tagging of MeCP2 reveals contextual insights into the Rett syndrome transcriptome

Mutations in MECP2 cause Rett syndrome (RTT), a X-linked neurological disorder characterized by the regressive loss of neurodevelopmental milestones and acquired intellectual disability and motor impairments. However, the cellular heterogeneity of the mammalian brain impedes our understanding of how MECP2 mutations disrupt neuronal function and contribute to RTT. In response, we developed cell type-specific biotin tagging in mice bearing RTT-associated mutations and profiled nuclear transcriptomes in WT and mutant neurons. Although individual gene expression changes are largely specific to each mutation and cell type, higher-level transcriptional features remain conserved and correlate with RTT phenotypic severity. Furthermore, subcellular RNA populations support post-transcriptional compensation as a basis for the upregulation of long genes previously reported in RTT mutant neurons. Finally, we overcame the genetic mosacism associated with female RTT mouse models and identified functionally distinct gene expression changes in neighboring WT and mutant neurons, which altogether provide key contextual insights into RTT. Nuclear total RNA-seq of two types of neurons of male and female RTT mice and GRO-seq of the cortexMECP2突变可引发雷特综合征（Rett syndrome, RTT），这是一类以神经发育里程碑退行性丧失、获得性智力障碍及运动功能受损为特征的X连锁神经疾病。然而，哺乳动物大脑的细胞异质性阻碍了我们解析MECP2突变如何扰乱神经元功能并促成RTT发病的研究。为此，我们在携带RTT相关突变的小鼠中构建了细胞类型特异性生物素标记体系，并对野生型（Wild Type, WT）与突变神经元的细胞核转录组开展了测序分析。尽管单个基因的表达变化在很大程度上具有突变类型与细胞类型特异性，但更高层级的转录组特征仍保持保守，且与RTT的表型严重程度显著相关。此外，亚细胞RNA群体的分析结果支持转录后补偿机制，该机制可作为此前报道的RTT突变神经元中长基因上调的理论基础。最后，我们攻克了雌性RTT小鼠模型固有的遗传嵌合性难题，并在相邻的野生型与突变神经元中鉴定出功能差异显著的基因表达变化，上述发现共同为RTT的研究提供了关键的情境化认知。本数据集涵盖雄性与雌性RTT小鼠两类神经元的细胞核总RNA测序（RNA-seq）数据，以及大脑皮层的全局run-on测序（Global Run-On Sequencing, GRO-seq）数据。