Foroozani M, Zahraeifard S, Oh DH, Wang G, Dassanayake M, Smith AP.

Plant Physiol. 2019 Dec 19. pii: pp.01153.2019. doi: 10.1104/pp.19.01153. [Epub ahead of print]

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.

See http://www.plantphysiol.org/content/early/2019/12/19/pp.19.01153.long

Figure 1: H3K4me3 abundance is predominantly associated with the transcription start site (TSS) and co-localizes with H2A.Z. Distribution of H3K4me3 (A) and H2A.Z (B) among four gene types in shoots from rice seedlings grown under control conditions. Control input reads were used for ChIP-Seq read normalization. PCG, protein coding genes; PG, pseudogenes; TE, non-expressed transposable element-related genes; TEG, expressed transposable element-related genes. (C) Scatter plot of read counts from H3K4me3 and H2A.Z samples (Pearson correlation = 0.77). (D) Venn diagram showing the number of H3K4me3- and H2A.Zenrichment peaks and the overlap.