Low-Phosphate Chromatin Dynamics Predict a Cell Wall Remodeling Network in Rice Shoots

• Published in: Plant physiology (Bethesda) 2020-03, Vol.182 (3), p.1494-1509
• Main Authors: Foroozani, Maryam, Zahraeifard, Sara, Oh, Dong-Ha, Wang, Guannan, Dassanayake, Maheshi, Smith, Aaron P
• Format: Article
• Language: English
• Subjects: Cell Wall - genetics; Cell Wall - metabolism; Chromatin - metabolism; Gene Expression Regulation, Plant; Oryza - genetics; Oryza - metabolism; Plant Proteins - genetics; Plant Proteins - metabolism; Plant Roots - genetics; Plant Roots - metabolism; Transcription Initiation Site - physiology
• ISSN: 0032-0889; 1532-2548
• DOI: 10.1104/PP.19.01153

Phosphorus (P) is an essential plant macronutrient vital to fundamental metabolic processes. Plant-available P is low in most soils, making it a frequent limiter of growth. Declining P reserves for fertilizer production exacerbates this agricultural challenge. Plants modulate complex responses to fluctuating P levels via global transcriptional regulatory networks. Although chromatin structure plays a substantial role in controlling gene expression, the chromatin dynamics involved in regulating P homeostasis have not been determined. Here we define distinct chromatin states across the rice ( ) genome by integrating multiple chromatin marks, including the H2A.Z histone variant, H3K4me3 modification, and nucleosome positioning. In response to P starvation, 40% of all protein-coding genes exhibit a transition from one chromatin state to another at their transcription start site. Several of these transitions are enriched in subsets of genes differentially expressed under P deficiency. The most prominent subset supports the presence of a coordinated signaling network that targets cell wall structure and is regulated in part via a decrease of H3K4me3 at transcription start sites. The P starvation-induced chromatin dynamics and correlated genes identified here will aid in enhancing P use efficiency in crop plants, benefitting global agriculture.