Phytochromes B1/B2 are major regulators of ripening-associated epigenome reprogramming in tomato fruits

Phytochrome-mediated light and temperature perception has been shown to be a major regulator of fruit development. Furthermore, chromatin remodelling via DNA demethylation has been described as a crucial mechanism behind the fruit ripening process; however, the molecular basis underlying the triggering of this epigenetic modification remains largely unknown. Here, through integrative analyses of the methylome, siRNAome and transcriptome of tomato fruits from and null mutants, we report that PHYB1 and PHYB2 control genome-wide DNA methylation during fruit development. The experimental evidence indicates that PHYB1B2 signal transduction is mediated by the coordinated expression of DNA methylases/demethylases, histone-modifying enzymes and chromatin remodelling factors, resulting in the transcriptional regulation of photosynthetic and ripening-associated genes. This new level of understanding provides insights into the orchestration of epigenetic mechanisms in response to environmental cues affecting agronomical traits.