Evidence of chromatin-mediated drought stress memory in tomato (Solanum lycopersicum)

Plants go through their entire life cycle exactly where the initial seed germinated and must rapidly respond and adjust to frequent environmental changes, including abiotic stresses. Among these, drought is a major environmental stressor that exerts adverse effects on plant growth, development and productivity. To cope with drought, plants modulate gene expression and metabolism through a variety of biochemical, molecular, genetic, and epigenetic mechanisms. Chromatin marks may provide a basis for epigenetic memory, integrating environmental cues with developmental programs and enabling plants to respond more efficiently to recurring stress or to prepare offspring for future assaults. To dissect drought-induced epigenetic memory, we employed an integrative omics approach combining a phenomics-based approach, transcriptome analyses and genome-wide profiling of histone modifications. For this purpose, two tomato cultivars - Lucariello and M82 - were subjected to severe-recurrent and mild prolonged drought stress, respectively. The effect of recurrent and severe drought stress on chromatin and its correlation with gene expression was investigated by analysing the dynamic of H3K4me3 enrichment by ChIP-Seq in Lucariello leaves during stress application and recovery. By comparing H3K4me3 enrichment and distribution with differentially expressed genes during recurrent stress and recovery, a correlation between changes in H3K4me3 and gene expression was found. This allowed the identification of different categories of stressmemory genes. In M82 a mild prolonged stress has been applied to plants in pre-flowering for two following seasons (2023 and 2024). To identify ‘epitargets’ of stress response, we focused on gene loci showing stress induced transcriptional and chromatin mark variation. To further investigate the effects of drought stress on chromatin organization and histone mark distribution (e.g. H3K4me3, H3K27me3, H3K36me3, H3K9me2) in M82, immunolocalization assays were performed on nuclei isolated from leaf tissues. Interestingly, immunofluorescence detection revealed an enrichment in H3K27me3 signal in nuclei of leaves subjected to both mild and severe drought. Accordingly, the dynamic of H3K27me3 was further investigated by ChIP-Seq in M82 during stress and recovery. Lastly, to functionally validate the role of chromatin remodelling in drought response, expression analyses of previously identified candidate memory genes were performed in knockdown mutants of Slhda19 and knockout mutants of Slddm1, which are impaired in HISTONE DEACETYLASE 19 (HDA19) and DNA methylation, respectively. Altogether, our holistic approach provides a genome-wide map of the interplay between genes and chromatin marks employed by plants to cope with drought stress, highlighting how chromatin dynamics may represent a key element in the establishment of stress memory.