Histone post-translational modification profiles during tomato fruit post-harvest

Tomato (Solanum lycopersicum L.) is the model system for investigating the molecular basis of ripening in fleshy fruits. Ripening is orchestrated by a complex regulative network including multiple transcription factors, ethylene signaling pathway, and epigenome changes. It is still unclear whether fruit ripening has to be regarded as a process of senescence or as a distinct process. We investigated the biological relevance of histone post-translational modifications (HMs) H3K4me3, H3K9/K14ac, and H3K27me3 in fruit post-harvest using ChIP-Seq. H3K4me3 and H3K9/K14ac are histone marks that positively correlate with gene expression while H3K27me3 plays a repressive role. In this study, HMs were mapped in fruit pericarp of Lucariello, a landrace with long shelf-life belonging to "Pomodorino del Piennolo del Vesuvio DOP". Three different time points have been analyzed: red ripe fruit (Breaker+8) coincident with the harvest, 60 and 150 days after harvest. Based on HM profiles, the genome was partitioned into eight chromatin states, which correspond to regions marked by only one HM, co-occurrence of HMs and unmarked regions. H3K27me3-only regions were strongly associated with repetitive sequences. Chromatin states marked by H3K4me3 and/or H3K9/K14ac were found to be associated with gene bodies and promoters. Based on chromatin state changes between time points, we estimated that 12% of chromatin is dynamic during post-harvest. One-third of the changes is related to gain/loss of H3K27me3 mark. We identified differentially enriched peaks of HMs. We focused on those at +/-2kb from predicted transcription start site regions that correlate with differentially expressed genes. Data gathering and interpretation are now being carried out to identify the relative contribution of HMs to transcriptional regulation in tomato fruit post-harvest.