Genome-wide analysis of DNA methylation in response to light and salt stress in a halophyte with single cell C4 pathway
Year: 2026
Type: article
Abstract: BACKGROUND AND AIMS: DNA methylation plays a crucial role in the plant stress response, particularly under abiotic stress. Suaeda aralocaspica, a halophyte with the C4 photosynthetic pathway within a single polarized cell, exhibits unique adaptations to environmental challenges. This study investigates cytosine methylation patterns in S. aralocaspica under dark, light recovery and NaCl stress (100 and 500 mM; N100 and N500), focusing on the methylation-mediated regulation of stress-responsive genes, including different phosphoenolpyruvate carboxylase genes (SaPEPCs). METHODS: Whole-genome bisulphite sequencing was used to investigate DNA methylation in different stress treatments. Gene expression and western blot analyses in photosynthesis and salt response pathways were conducted after treatment with a DNA methylation inhibitor (5-azacytidine) and a methylating agent (methyl trifluoromethanesulphonate) to assess the functional link between methylation and gene regulation. KEY RESULTS: Global methylation levels in S. aralocaspica decreased under stress, with non-CG methylation showing the most significant changes. The majority of 81 854 and 14 653 differentially methylated regions (under N500 and darkness, respectively, were hypomethylated. Dynamic DNA methylation directly regulates the expression of genes involved in both photosynthetic and salt stress responses. In most cases, mRNA expression of these genes increased when their promoters were hypomethylated. The functional significance of these methylation patterns was confirmed using the DNA methylation inhibitor or DNA methylating agent. These treatments revealed that hypomethylation can enhance gene expression, as observed in key genes, such as SaPEPC1, SaPEPC2, PPDK, CPK3 and CPK4. Between the two SaPEPC genes, SaPEPC2 showed differentially hypomethylated regions specifically in N500 treatment; in contrast, SaPEPC1 exhibited a differentially hypomethylated region in darkness. Combined with our previous study, our results suggest a functional divergence among these paralogues, and SaPEPC1 might be the key gene in carbon fixation. CONCLUSIONS: This study revealed a stress-induced genome-wide DNA hypomethylation in S. aralocaspica. SaPEPC1 and SaPEPC2 exhibited distinct methylation responses to darkness and salt stress, respectively. Through methylation alteration experiments, we established the associations between DNA methylation and relevant gene expression, which should improve our understanding of epigenetic regulation in halophyte stress adaptation.
Source: Annals of Botany
DOI: 10.1093/aob/mcag009
Authors: Jie Yang, Haiyan Lan
Institution: Xinjiang University
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: green
Award: G4282804383
OpenAlex ID: W7125704086