Title: DNA methylation is involved in acclimation to iron deficiency in rice (Oryza sativa)

Shuo Sun, Jiamei Zhu, Runze Guo, James Whelan, Huixia Shou

First published: 12 May 2021

https://doi.org/10.1111/tpj.15318

Summary

Iron (Fe) is an essential micronutrient in plants and Fe limitation significantly affects plant growth, yield and food quality. While many studies have reported the transcriptomic profile and pursue molecular mechanism in response to Fe limitation, little is known if epigenetic factors play a role in response to Fe deficiency. In this study, whole-genome bisulfite sequencing analysis, high throughput RNA-seq of mRNA, small RNA and transposable element (TE) expression with root and shoot organs of rice seedlings under Fe-sufficient and Fe-deficient conditions were performed. The results showed that widespread hypermethylation, especially for the CHH context, occurred after Fe deficiency. Integrative analysis of methylation and transcriptome revealed that the transcript abundance of Fe deficiency induced genes were negatively correlated with nearby TEs and positively with the 24-nt siRNAs. The ability of methylation to affect the physiology and molecular response to Fe deficiency was tested using an exogenous DNA methyltransferase inhibitor (5-azacytidine), and genetically using a mutant for DOMAINS REARRANGED METHYLTRANSFERASE 2 (DRM2), that lacks CHH methylation. Both approaches resulted in decreased growth and Fe content in rice plants. Thus, alterations in specific methylation patterns, directed by siRNAs play an important role in acclimation of rice to Fe deficient conditions. Furthermore, comparison with other reports suggests this may be a universal mechanism to acclimate to limited nutrient availability.

Link:  https://onlinelibrary.wiley.com/doi/10.1111/tpj.15318