Chromatin accessibility dynamics and transcriptional regulatory networks underlying the primary nitrogen response in rice roots

Abstract

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.