(RNA-seq-SHSY5Y) Hao-Fountain syndrome protein USP7 mediates neuronal differentiation via BCOR-ncPRC1.1. (RNA-seq-SHSY5Y) Hao-Fountain syndrome protein USP7 mediates neuronal differentiation via BCOR-ncPRC1.1

Pathogenic variants of ubiquitin-specific protease 7 (USP7) cause the neurodevelopmental disorder Hao-Fountain syndrome. However, which of its pleiotropic substrates are relevant for neurodevelopment has remained unclear. Here, we present a combination of quantitative proteomics, transcriptomics and epigenomics to define the core USP7 circuitry during neurodifferentiation. USP7 activity is required for the transcriptional programs that direct the differentiation of human ESCs to neural stem cells, and neuronal differentiation of SHSY5Y neuroblastoma cells. In addition to other substrates, including TRIM27, USP7 controls the dosage of the Polycomb H2AK119ub1 ubiquitin ligases ncPRC1.1 and ncPRC1.6. We found that BCOR-ncPRC1.1, but not ncPRC1.6 or TRIM27, is a key effector of USP7-dependent neuronal differentiation. Indeed, BCOR-ncPRC1.1 mediates the majority of USP7-dependent gene regulation during this process. Besides providing a detailed map of the USP7 regulome during neuronal differentiation, our results suggest that Hao-Fountain syndrome and ncPRC1.1-associated neurodevelopmental disorders involve dysregulation of a shared epigenetic network. Overall design: RNA-seq in SHSY5Y neuroblastoma treated with USP7 inhibitor, or deleted for p53, BCOR, or USP7

泛素特异性蛋白酶7（ubiquitin-specific protease 7，USP7）的致病变异可引发神经发育障碍Hao-Fountain综合征。然而，其众多多效底物中哪些与神经发育相关，目前仍不明确。本研究结合定量蛋白质组学（quantitative proteomics）、转录组学（transcriptomics）与表观基因组学（epigenomics）技术，解析神经分化过程中USP7的核心调控网络。USP7的活性对于调控人类胚胎干细胞（human embryonic stem cells，ESCs）向神经干细胞分化，以及SHSY5Y神经母细胞瘤细胞的神经元分化的转录程序不可或缺。除TRIM27等其他底物外，USP7还可调控多梳家族（Polycomb）H2AK119ub1泛素连接酶ncPRC1.1与ncPRC1.6的蛋白剂量。研究发现，BCOR-ncPRC1.1而非ncPRC1.6或TRIM27，是USP7依赖型神经元分化的关键效应因子。实际上，在此过程中，BCOR-ncPRC1.1介导了USP7依赖型基因调控的绝大多数事件。本研究不仅绘制了神经元分化过程中USP7调控组（regulome）的详细图谱，还提示Hao-Fountain综合征与ncPRC1.1相关的神经发育障碍可能存在共同的表观遗传网络失调。整体实验设计：对经USP7抑制剂处理，或敲除p53、BCOR或USP7的SHSY5Y神经母细胞瘤细胞进行RNA测序（RNA-seq）。