Given the difficulties of obtaining diseased cells, differentiation of neurons from patient-specific human induced pluripotent stem cells (iPSCs) with neural progenitor cells (NPCs) as intermediate precursors is of great interest. While cellular and transcriptomic changes during the differentiation process have been tracked, little attention has been given to examining spatial re-organization, which has been revealed to control gene regulation in various cells. To address the regulatory mechanism by 3D chromatin structure during neuronal differentiation, we examined the changes that take place during differentiation process using two cell types that are highly valued in the study of neurodegenerative disease - iPSCs and NPCs. In our study, we used Hi-C, a derivative of chromosome conformation capture that enables unbiased, genome-wide analysis of interaction frequencies in chromatin. We showed that while topologically associated domains remained mostly the same during differentiation, the presence of differential interacting regions in both cell types suggested that spatial organization affects gene regulation of both pluripotency maintenance and neuroectodermal differentiation. Moreover, closer analysis of promoter-promoter pairs suggested that cell fate specification is under the control of cis-regulatory elements. Our results are thus a resourceful addition in benchmarking differentiation protocols and also provide a greater appreciation of NPCs, the common precursors from which required neurons for applications in neurodegenerative diseases such as Parkinson's disease, Alzheimer's disease, schizophrenia and spinal cord injuries are utilized.

中文翻译：

---

iPSC-NPC 模型期间染色质相互作用的变化有助于研究参与分化的具有生物学意义的基因


鉴于获得患病细胞的困难，以神经祖细胞（NPC）作为中间前体，从患者特异性人诱导多能干细胞（iPSC）中分化出神经元引起了人们的极大兴趣。虽然已经追踪了分化过程中的细胞和转录组变化，但很少有人关注空间重组的研究，而空间重组已被证明可以控制各种细胞中的基因调控。为了解决神经元分化过程中 3D 染色质结构的调节机制，我们使用在神经退行性疾病研究中高度重视的两种细胞类型 - iPSC 和 NPC，检查了分化过程中发生的变化。在我们的研究中，我们使用了 Hi-C，这是一种染色体构象捕获的衍生物，能够对染色质相互作用频率进行公正的全基因组分析。我们发现，虽然拓扑相关结构域在分化过程中基本保持不变，但两种细胞类型中存在差异相互作用区域表明空间组织影响多能性维持和神经外胚层分化的基因调控。此外，对启动子-启动子对的更仔细分析表明，细胞命运规范受到顺式调控元件的控制。因此，我们的结果为基准分化方案提供了丰富的补充，并且还提供了对 NPC 的更好的认识，NPC 是神经退行性疾病（如帕金森病、阿尔茨海默病、精神分裂症和脊髓损伤）应用所需神经元的常见前体。