Plasticity of DNA methylation and gene expression under zinc deficiency in Arabidopsis roots

Abstract

DNA methylation is a heritable chromatin modification that maintains chromosome stability, regulates transposon silencing and appears to be involved in gene expression in response to environmental conditions. Environmental stress alters DNA methylation patterns that are correlated with gene expression differences. Here, genome-wide differential DNA-methylation was identified upon prolonged Zn deficiency, leading to hypo- and hyper-methylated chromosomal regions. Preferential CpG methylation changes occurred in gene promoters and gene bodies, but did not overlap with transcriptional start sites. Methylation changes were also prominent in transposable elements. By contrast, non-CG methylation differences were exclusively found in promoters of protein coding genes and in transposable elements. Strongly Zn deficiency-induced genes and their promoters were mostly non-methylated, irrespective of Zn supply. Differential DNA methylation in the CpG and CHG, but not in the CHH context, was found close to a few up-regulated Zn-deficiency genes. However, the transcriptional Zn-deficiency response in roots appeared little correlated with associated DNA methylation changes in promoters or gene bodies. Furthermore, under Zn deficiency, developmental defects were identified in an Arabidopsis mutant lacking non-CpG methylation. The root methylome thus responds specifically to a micro-nutrient deficiency and is important for efficient Zn utilization at low availability, but the relationship of differential methylation and differentially expressed genes is surprisingly poor.

Epigenetic regulation in plant abiotic stress responses

“…Mutation in MORE SULPHUR ACCUMULATION1 (MSA1), which is required for the biosynthesis of the universal methyl donor S‐adenosylmethionine (SAM), resulted in a global reduction of DNA methylation levels and changes of gene expression, including SULTR1.1 and SULTR1.2 (Huang et al 2016). More recently, Chen et al identified the genome‐wide DNA methylation change upon prolonged Zn deficiency and demonstrated that differential DNA methylation in the CpG and CHG, but not CHH context, was related to the upregulation of a few Zn deficiency‐responsive genes (Chen et al 2018). Interestingly, the ddc ( drm1/drm2/cmt3 ) mutant, which lacks non‐CG methylation, displayed more severe developmental defects under Zn deficiency (Chen et al 2018).…”

“…More recently, Chen et al identified the genome‐wide DNA methylation change upon prolonged Zn deficiency and demonstrated that differential DNA methylation in the CpG and CHG, but not CHH context, was related to the upregulation of a few Zn deficiency‐responsive genes (Chen et al 2018). Interestingly, the ddc ( drm1/drm2/cmt3 ) mutant, which lacks non‐CG methylation, displayed more severe developmental defects under Zn deficiency (Chen et al 2018). These results indicated a connection between the Zn deficiency response and DNA methylation dynamics.…”

Genetic and Global Epigenetic Modification, Which Determines the Phenotype of Transgenic Rice?

“…DNA methylation is an epigenetic mechanism that involves the transfer of a methyl group to the C5 position of cytosine and contributes to the epigenetic regulation of nuclear gene expression and to genome stability [16]. In plants, DNA methylation occurs in three sequence contexts: CG, CHG, and CHH (H=A, C or T) [16,17]. The modulation of DNA methylation in culture is crucial to regeneration outcomes: successful regenerants of Oryza sativa ssp.…”

Epigenetic Mechanisms of Plant Adaptation to Biotic and Abiotic Stresses

“…In a zinc (Zn) deficiency tolerant Arabidopsis genotype Sf-2, a prolonged Zn deficiency treatment upregulated 189 and downregulated 430 genes more than twofold [ 61 ]. The Zn transporter family genes ZIP1 , ZIP3 , ZIP4 , ZIP5 , and IRT3 , the nicotianamine synthase genes NAS2 and NAS4 , the heavy metal ATPase gene HMA2 , and the purple acid phosphatase gene PAP27 were among the most robustly induced genes.…”