Adverse environmental conditions reduce crop productivity and often increase the load of unfolded or misfolded proteins in the endoplasmic reticulum (ER). This potentially lethal condition, known as ER stress, is buffered by the unfolded protein response (UPR), a set of signaling pathways designed to either recover ER functionality or ignite programmed cell death. Despite the biological significance of the UPR to the life of the organism, the regulatory transcriptional landscape underpinning ER stress management is largely unmapped, especially in crops. To fill this significant knowledge gap, we performed a large‐scale systems‐level analysis of the protein–DNA interaction (PDI) network in maize (Zea mays). Using 23 promoter fragments of six UPR marker genes in a high‐throughput enhanced yeast one‐hybrid assay, we identified a highly interconnected network of 262 transcription factors (TFs) associated with significant biological traits and 831 PDIs underlying the UPR. We established a temporal hierarchy of TF binding to gene promoters within the same family as well as across different families of TFs. Cistrome analysis revealed the dynamic activities of a variety of cis‐regulatory elements (CREs) in ER stress‐responsive gene promoters. By integrating the cistrome results into a TF network analysis, we mapped a subnetwork of TFs associated with a CRE that may contribute to UPR management. Finally, we validated the role of a predicted network hub gene using the Arabidopsis system. The PDIs, TF networks, and CREs identified in our work are foundational resources for understanding transcription‐regulatory mechanisms in the stress responses and crop improvement.

中文翻译：

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时间层次结构支撑了玉米 UPR 的转录因子-DNA 相互作用组

不利的环境条件会降低作物生产力，并经常增加内质网 (ER) 中未折叠或错误折叠蛋白质的负载。这种潜在的致命条件，称为内质网应激，由未折叠蛋白反应 (UPR) 缓冲，这是一组旨在恢复内质网功能或点燃程序性细胞死亡的信号通路。尽管 UPR 对生物体的生命具有生物学意义，但支持 ER 压力管理的调控转录景观在很大程度上尚未确定，尤其是在作物中。为了填补这一重大的知识空白，我们对玉米（Zea mays）。在高通量增强型酵母单杂交试验中使用六个 UPR 标记基因的 23 个启动子片段，我们确定了一个高度互连的网络，该网络由与重要生物学特性相关的 262 个转录因子 (TF) 和 UPR 基础的 831 个 PDI 组成。我们建立了 TF 与同一家族内以及不同 TF 家族中基因启动子结合的时间层次结构。Cistrome 分析揭示了多种顺式的动态活动内质网应激反应基因启动子中的调节元件（CRE）。通过将 cistrome 结果整合到 TF 网络分析中，我们绘制了一个与可能有助于 UPR 管理的 CRE 相关联的 TF 子网。最后，我们使用拟南芥系统验证了预测的网络枢纽基因的作用。我们工作中发现的 PDI、TF 网络和 CRE 是理解应激反应和作物改良中转录调控机制的基础资源。