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Updated: Sep 19, 2025

Plant Promoter Analysis: Identification and Characterization of Root Nodule Specific Promoter in the Common Bean
Published on: December 23, 2017
Chromatin accessibility dynamics and transcriptional regulatory networks underlying the primary nitrogen response in
Wenhui Li1, Xinxin Zhu1, Junjiao Yang1
1National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China.
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.
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Transcription
Transcription is the process of synthesizing RNA from a DNA sequence by RNA polymerase. It is the first step in producing a protein from a gene sequence. Additionally, many other proteins and regulatory sequences are involved in the proper synthesis of messenger RNA (mRNA). Regulation of transcription is responsible for the differentiation of all the different types of cells and often for the proper cellular response to environmental signals.
Transcription Can Produce Different Kinds...
Stringent Response in E. coli
Cell Signaling in Plants
RNA Polymerase II Accessory Proteins
Co-activators and Co-repressors
Key Elements for Plant Nutrition