Li Wenhui, Zhu Xinxin, Yang Junjiao, Zhou Xiangyu, Ming Luchang, Yang Ling, Li Jiacheng, Tan Zengdong, Xia Chunjiao, Wang Dujun, Xu Xingbing, Zong Zhanxiang, Zhao Hu, Yang Meng, Xiong Lizhong, Lian Xingming, Xie Weibo
National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China.
State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Agriculture, Guangxi University, Nanning, China.
Plant Commun. 2025 Jul 14;6(7):101392. doi: 10.1016/j.xplc.2025.101392. Epub 2025 Jun 3.
Nitrogen (N) is essential for rice growth; however, the transcriptional regulation of the primary nitrogen response (PNR), characterized by the rapid upregulation of N uptake and assimilation genes upon N resupply, remains poorly understood. This study investigated the dynamics of the PNR in the roots of two rice cultivars (Zhenshan 97 and Nipponbare) via time-series Assay for Transposase-Accessible Chromatin using sequencing and RNA sequencing analyses within 2 h of ammonium nitrate resupply. Regulatory regions responsive to N induction were precisely identified. Coordinated and cascading changes in chromatin accessibility and gene expression were observed, with chromatin state frequently preceding transcriptional changes. Integrative analysis of expression-chromatin accessibility associations revealed a redundant N-responsive regulatory network. OsLBD38 and OsLBD39, identified as early-response regulators, transcriptionally suppress nitrate reductases while enhancing nitrite reductases; they may function as metabolic safeguarders to prevent nitrite accumulation. OsbZIP23 was identified as a novel regulator directly binding to the promoters of N uptake and metabolism genes, regulating genes in patterns opposite to LBD-regulated genes, suggesting a complex regulatory interplay. Cross-species comparisons with Arabidopsis highlighted the conserved N-responsive regulatory roles of these hub regulators and their targets. Comparative analyses between cultivars revealed expression divergence and genetic differentiation in N-responsive genes, implying indica/japonica-specific adaptations. Furthermore, deep learning predictions of chromatin accessibility between cultivars indicated that expression variation in N uptake and metabolism genes is primarily influenced by trans-acting regulatory factors. These findings provide a comprehensive view of the dynamic regulatory landscape governing the PNR in rice.
氮（N）对水稻生长至关重要；然而，初级氮响应（PNR）的转录调控，其特征是在重新供应氮后氮吸收和同化基因迅速上调，目前仍知之甚少。本研究通过在重新供应硝酸铵后2小时内进行的基于测序的转座酶可及染色质时间序列分析和RNA测序分析，研究了两个水稻品种（珍汕97和日本晴）根中PNR的动态变化。精确鉴定了对氮诱导有响应的调控区域。观察到染色质可及性和基因表达的协调和级联变化，染色质状态变化通常先于转录变化。对表达-染色质可及性关联的综合分析揭示了一个冗余的氮响应调控网络。被鉴定为早期响应调节因子的OsLBD38和OsLBD39在转录水平上抑制硝酸还原酶，同时增强亚硝酸还原酶；它们可能作为代谢保护因子来防止亚硝酸盐积累。OsbZIP23被鉴定为一种新型调节因子，直接结合到氮吸收和代谢基因的启动子上，以与LBD调节基因相反的模式调节基因，表明存在复杂的调控相互作用。与拟南芥的跨物种比较突出了这些核心调节因子及其靶标的保守氮响应调控作用。品种间的比较分析揭示了氮响应基因的表达差异和遗传分化，这意味着籼稻/粳稻特异性适应。此外，对品种间染色质可及性的深度学习预测表明，氮吸收和代谢基因的表达变异主要受反式作用调控因子影响。这些发现提供了水稻中PNR动态调控格局的全面视图。
