Abstract
Glucosinolates (GSLs) are secondary metabolites central to plant defence in the Brassicaceae family. While the role of histone modifications in developmental gene regulation is well studied, their function in stress-induced secondary metabolism remains unclear. Here, we show that GSL biosynthetic genes in Arabidopsis thaliana are regulated by bivalent chromatin bearing both active (histone acetylation) and repressive (H3K27me3) histone marks. Components of the Polycomb Repressive Complex 2 (PRC2), including CLF, SWN and LHP1, suppress GSL gene expression, and their loss enhances GSL accumulation. Genome-wide analyses revealed that indolic and aliphatic GSL genes are enriched with H3K27me3, with indolic genes also marked by active histone acetylation. Time-course transcriptome and metabolite analyses using HPLC following wounding revealed distinct temporal activation patterns, with indolic GSL genes induced during the early phases and aliphatic GSL genes activated at later stages. These findings suggest that bivalent histone modifications orchestrate temporal gene expression of GSL pathways under stress, revealing a previously unrecognised epigenetic mechanism underlying plant metabolic responses to environmental stimuli.