Abstract
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 (Oryza sativa) 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.
Highlights
Phosphorus (P) is among the most limiting essential nutrients for plants because the primary plant-available form of P, inorganic phosphate (Pi), has poor solubility in most soils (Holford, 1997)
We began by determining the genome distribution of H3K4me3 via chromatin immunoprecipitation (ChIP)-seq on shoots from 36-day-old rice
Genes were categorized into four groups based on the MSU7 genome annotation: protein-coding genes (PCG), ‘pseudogenes’
Summary
Phosphorus (P) is among the most limiting essential nutrients for plants because the primary plant-available form of P, inorganic phosphate (Pi), has poor solubility in most soils (Holford, 1997). In order to tolerate low-Pi conditions and maintain optimal P levels, plants have evolved a number of physiological, morphological, and biochemical responses, such as reduced growth, altered root system architecture, and secretion of organic acids, phosphatases, and nucleases to acquire more Pi (Secco et al, 2013). These responses are modulated by large transcriptional networks in which the MYB protein PHOSPHATE STARVATION RESPONSE 1 (PHR1) and related transcription factors play key roles (Secco et al, 2013, Sun et al, 2016)
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