GSE128041
Global epigenome analysis reveals the role of histone modifications in the chilling-regulated gene expressions in dormant apple flower buds
Bud dormancy – the repeated phase of rest that punctuates periods of growth in the life cycles of many perennial species. In temperate fruit trees, fulfillment of chilling requirement and subsequent heat requirement enable dormant buds to have uniform blooming in field. However, effects of environmental factors such as chilling underlying dormancy release and bud break has not been fully understood. Histone modification is an important epigenetic regulation system which plays an important role in gene expression in various developmental and adaptive processes. Taking advantage of next-generation sequencing, we generated epigenome and transcriptome profiling at different stages before chilling, after chilling and just before bud break in apple (Malus x domestica). We found H3K27me3 may play dominant role during chilling and the genes involved in lignin and lipid metabolic process showed histone modifications. Interestingly, the higher ratio of genes in chilling-associated network exhibited histone modifications, suggesting crucial epigenetic roles in regulating gene expressions in response to chilling during dormancy. Furthermore, H3K4me3 may play more important role during bud break and the genes related to cell wall modification/organization were strongly modified. Taken together, this study provides important insights into the chromatin-based gene regulation underlying chilling-mediated dormancy release and bud break in apple. Overall design: We conducted ChIP-seq using terminal buds at three stages, buds before chilling exposure (sample “BC”) and after chilling exposure (sample “AC”), buds after chilling exposure then under forcing condition before bud break (sample “BB”), using antibodies against H3K27me3 and H3K4me3, and both H3 and Input were used as standard control. All sample were did with two biology replicates (_rep1 and _rep2).