The Role of Chromatin State Transitions in Modulating Early Phosphate-deficiency Response Genes in Plants

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-level mechanisms involved in regulating P homeostasis have not been determined. In this work, I used chromatin immunoprecipitation (ChIP) combined with next-generation DNA sequencing (ChIP-seq) to map the distribution of H3K4me3 in rice (Oryza sativa L.) during both control and P-deficient conditions, and also used RNA-seq analyses to investigate global gene expression under the same set of conditions. In addition, I integrated multiple aspects of chromatin structure to define distinct chromatin states across the rice genome and compared them with profiles of genes differentially expressed by P deficiency. Finally, I investigated the potential role of the Arabidopsis SDG2 histone methyltransferase in P homeostasis. The results of this work reveal that chromatin structure plays a valuable role in modulating gene expression in response to P-deficiency. First, I showed that H3K4me3 is prominent at the 5’ end of rice protein-coding genes, that it co-localizes with the H2A.Z histone variant, and the abundance of both H3K4me3 and H2A.Z exhibit distinct correlations with gene expression. Second, I defined distinct chromatin states across the rice genome by integrating the distribution of H3K4me3, H2A.Z, and nucleosome positioning. In response to P deficiency, 40% of all protein-coding genes exhibit a chromatin state transition, and 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 loss of transcription start site-localized H3K4me3. Finally, I showed that there was significant overlap between genes differentially expressed by P deficiency and those differentially expressed in an Arabidopsis sdg2 mutant. The P-deficiency induced chromatin dynamics and correlated genes identified here will be used in future efforts to generate crop plants exhibiting enhanced P-use efficiency, which is critical for sustaining global agriculture.