The H3K27me3 histone mark correlates with repression of colour and aroma development post-harvest in strawberry fruit

Strawberry ripening is non-climacteric, and post-harvest fruit enter senescence and deteriorate rapidly. Chilled storage induces transcriptome wide changes in gene expression, including the down-regulation of aroma related genes. Histone marks are associated with transcriptional activation or repression; the H3K27me3 mark is mainly associated with repression of gene expression. Here genes associated with H3K27me3 were identified through ChIP-seq in ripe red strawberry fruit at harvest and after 5 days of chilled storage in the dark. The number of ChIP peaks increased with storage time, indicating an increased role for this mark in regulation of gene expression following chilled dark storage. Comparing ChIP-seq data to RNA-seq data from the same material identified 440 genes whose expression correlates with H3K27me3 repression. Abiotic stress genes, especially cold stress response genes, were down-regulated during storage. Increased association with the H3K27me3 mark indicates that they may be repressed via this epigenetic mark. Other functional groups included cell wall and carbohydrate metabolism. The association with the H3K27me3 mark of two transcription factors (FaHY5 and FaTRAB1) and FaADH, involved in ester biosynthesis, was validated by ChIP-PCR. These three genes are all down-regulated during storage and indicate a network of H3K27me3 gene repression affecting both anthocyanin and ester biosynthesis.