CUT&tag analysis reveals a crucial role of H3K4 trimethylation occupancy in cold-related genes by cold stress on cotton

Cotton originated in the tropics and is sensitive to low temperatures. Low-temperature stress has always been a significant limiting factor restricting its domestication and spread. The H3K4me3 histone mark regulates plant gene expression and transcriptional memory while influencing several developmental processes and stress responses. However, the potential function of cold stress-induced H3K4 trimethylation of cold-related genes in cotton’s response to cold is mostly underinvestigated. Here, we found that low temperatures significantly alter the levels of H3K4me3 modification in cotton, and the levels of H3K4me3 modification significantly correlate with the expression levels of cold-responsive genes. H3K4me3 modification has a role in regulating the expression of positive or negative cold-responsive genes, with positive regulation predominant in upland cotton (71.1%). 5182 core cold-induced genes marked by H3K4me3 (CCRGs), including the crucial cold signaling regulatory pathway ICE-CBF-CORs, have been identified. We revealed that within the ICE-CBF-CORs regulatory pathway, ICE1, CBF1, and most COR genes are positively regulated by H3K4me3. Weighted Gene Co-expression Network Analysis (WGCNA) analysis demonstrated that the expression patterns of CCRG genes are significantly correlated with the elongation of cotton radicles under low temperatures. We conducted preliminary functional validation of cold-responsive gene GhZAT11 modified by H3K4me3 and found that its silencing significantly reduces the cold tolerance of cotton. This supports the application of CCRG genes in cold tolerance research in cotton.