Genome-wide analysis of H3K27me3 in cucumber during recovery after cold stress priming

Plants can develop an epigenetic cold stress memory through priming (CS-P), which enhances their future tolerance, yet the genome-wide dynamics of H3K27me3 underlying this process were previously unknown. In this study, the cucumber leaf samples under normal condition and 4 h and 48 h during recovery after CS-P were collected. Three independent plants were pooled as one biological replicate, and the experiment was repeated twice for ChIP-sequence with IDR (Irreproducible Discovery Rata) analysis. Our study revealed that following CS-P, the distribution of H3K27me3 modifications in the cucumber genome underwent a characteristic shift: peaks ≤1000 bp decreased while larger peaks increased, a change aligned with enhanced signal intensity during recovery that demonstrates a hallmark of epigenetic memory. At the gene level, H3K27me3 signal decreased on most cold-induced genes during recovery, lifting the repression on their expression. While H3K27me3 deposition did not directly correlate with cold-induced gene expression globally, indicating multifactorial control. The H3K27me3 configuration on cold stress memory genes was crucial for transcriptional memory, exhibiting lower modification on up-memory genes to facilitate sustained expression and higher modification on down-memory genes to enforce sustained repression. In contrast, H3K27me3 persistently suppressed non-sustainably induced (NSI) genes, promoting expression reversion. These regulatory rules were found to be independent of the CS-P treatment itself. Importantly, we also found that H3K27me3 modified genes were mainly non-sustainably induced (NSI) genes related to redox and antioxidant substances. In summary, this work elucidates the post-recovery H3K27me3 dynamics governing cold-induced genes, providing a foundational understanding for improving cold tolerance in cucumber.