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 exasperates 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 aspects of chromatin structure, 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 by 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 the transcription start site. The P-starvation induced chromatin dynamics and correlated genes identified here will aid in enhancing P-use efficiency in crop plants, benefitting global agriculture.
One sentence summary Combining data for three components of chromatin structure from control and phosphate-starved rice shoots reveals specific chromatin state transitions that correlate with subsets of functionally distinct differentially-expressed genes.
Footnotes
Author contributions: M.F. performed the experiments, analyzed the data, and wrote the article; S.Z provided technical assistance; D-H.O. and G.W. provided bioinformatics assistance; M.D. supervised the data analysis; A.S. conceived the project, supervised the experiments and data analysis, complemented the writing, and agrees to serve as the author responsible for contact and ensure communication
Funding information: Funding was provided by a Plant Genome Research Program grant from the National Science Foundation (IOS-1127051).
Author for contact: A. Smith, apsmith{at}lsu.edu