Cellular differentiation requires dramatic changes in chromatin organization, transcriptional regulation, and protein production. To understand the regulatory connections between these processes, we generated proteomic, transcriptomic, and chromatin accessibility data during differentiation of mouse embryonic stem cells (ESCs) into postmitotic neurons and found extensive associations between different molecular layers within and across differentiation time points. We observed that SOX2, as a regulator of pluripotency and neuronal genes, redistributes from pluripotency enhancers to neuronal promoters during differentiation, likely driven by changes in its protein interaction network. We identified ATRX as a major SOX2 partner in neurons, whose co-localization correlated with an increase in active enhancer marks and increased expression of nearby genes, which we experimentally confirmed for three loci. Collectively, our data provide key insights into the regulatory transformation of SOX2 during neuronal differentiation, and we highlight the significance of multi-omic approaches in understanding gene regulation in complex systems.

细胞分化需要染色质组织、转录调控和蛋白质产生的巨大变化。为了了解这些过程之间的调控联系，我们在小鼠胚胎干细胞 (ESC) 分化为有丝分裂后神经元期间生成了蛋白质组学、转录组学和染色质可及性数据，并发现了分化时间点内和跨分化时间点不同分子层之间的广泛关联。我们观察到 SOX2 作为多能性和神经元基因的调节剂，在分化过程中从多能性增强子重新分配到神经元启动子，这可能是由其蛋白质相互作用网络的变化驱动的。我们将 ATRX 确定为神经元中主要的 SOX2 伙伴，其共定位与活性增强子标记的增加和附近基因的表达增加相关，我们通过实验证实了三个基因座。总的来说，我们的数据为神经元分化过程中 SOX2 的调控转化提供了关键见解，我们强调了多组学方法在理解复杂系统中的基因调控方面的重要性。