• Salt stress triggers genome-wide H3K27me3 erasure in cotton roots. • RDS 3434 treatment lowers H3K27me3 and enhances salt tolerance in cotton plants. • 36 genes show inverse H3K27me3/expression dynamics under salt stress. • GhNCED3 and GhTIFY9 modulate Na + /K + homeostasis to improve cotton salt tolerance. Histone modifications are among the key epigenetic regulators of gene expression in plants under abiotic stress, particularly in modulating stress responses by activating or repressing specific genes. Nevertheless, the epigenetic basis of the salt stress response in cotton remains largely unknown, despite its comparative salt tolerance. This study aimed to decode the genome-wide histone H3 lysine 27 trimethylation (H3K27me3) regulatory landscape in cotton under salt stress, establish the relationship between H3K27me3 dynamics and stress resilience, and identify epigenetically controlled target genes with breeding potential. Cleavage under targets and tagmentation (CUT&Tag) and RNA sequencing (RNA-Seq) were employed to profile the genome-wide distribution of H3K27me3 and its associated gene expression changes in cotton roots under salt stress. Exogenous application of the H3K27me3 inhibitor RDS 3434 was used to assess its impact on H3K27me3 levels and salt tolerance. Virus-induced gene silencing (VIGS) was employed to validate candidate genes regulated by H3K27me3 under salt stress. Salt stress significantly reduced H3K27me3 levels in cotton roots, and RDS 3434 treatment further decreased H3K27me3 deposition while enhancing salt tolerance. Genome-wide analysis revealed the expression of 36 genes was negatively correlated with H3K27me3 levels under salt stress. VIGS experiments verified two key genes, GhNCED3 and GhTIFY9 , whose H3K27me3 levels were down-regulated and expression levels up-regulated under salt stress, positively contributing to salt tolerance by modulating reactive oxygen species (ROS) accumulation and Na + /K + balance in cotton seedlings. This study provides evidence for the critical role of H3K27me3 in modulating gene expression for salt tolerance in cotton. The findings highlight the epigenetic regulation of salt tolerance and identify GhNCED3 and GhTIFY9 as promising candidates for developing salt-tolerant cotton cultivars. These insights advance our understanding of H3K27me3-mediated epigenetic regulation of abiotic stress adaptation in plants and provide a foundation for future crop improvement strategies.
Liu et al. (Sun,) studied this question.