Effects of Nr6a1 overexpression in neural progenitors at the chromatin level [ATAC-seq]

The vertebrate neural tube generates a large diversity of molecularly and functionally distinct neurons and glia from a small progenitor pool. While the role of spatial patterning in organising cell fate specification has been extensively studied, temporal patterning, which controls the timing of cell type generation, is equally important. Here we define a global temporal programme in the spinal cord. This governs cell fate choices by regulating chromatin accessibility in neural progenitors. Perturbation of this cis-regulatory programme affects sequential transitions in spinal cord progenitors and the identity of progeny. The temporal programme operates in parallel to spatial patterning, ensuring the timely availability of regulatory elements for spatial determinants to direct cell-type specific gene expression. These findings identify a chronotopic spatiotemporal integration strategy in which a global temporal chromatin programme determines the output of a spatial gene regulatory network resulting in the temporally and spatially ordered allocation of cell type identity. Overall design: ATACseq of mouse neural progenitor at day 9 in the differentiation protocol overexpressing either control or Nr6a1.

脊椎动物神经管可由少量祖细胞库生成分子特征与功能特性各异的海量神经元及神经胶质细胞。尽管学界已对空间模式化（spatial patterning）在调控细胞命运特化（cell fate specification）中的作用开展了广泛研究，但控制细胞类型生成时序的时间模式化（temporal patterning）同样至关重要。本研究明确了脊髓中的全局性时间程序：该程序通过调控神经祖细胞的染色质可及性（chromatin accessibility），支配细胞命运选择过程。该顺式调控程序（cis-regulatory programme）的扰动会干扰脊髓祖细胞的时序转变及其子代细胞的身份特性。该时间程序与空间模式化协同运作，确保空间决定因子（spatial determinants）能够及时获取调控元件，进而指导细胞类型特异性基因的表达。本研究揭示了一种时空拓扑整合策略（chronotopic spatiotemporal integration strategy）：全局性时间染色质程序决定空间基因调控网络的输出结果，最终实现细胞类型身份在时间与空间维度上的有序分配。
实验整体设计：对分化方案中第9天的小鼠神经祖细胞进行ATAC-seq测序，该细胞分别过表达对照（空载体）与Nr6a1基因。