Hydrogen boosts phenolic biosynthesis in germinated brown rice by regulating chromatin accessibility, mitochondrial redox and TCA cycle.

Germination is an effective strategy to enrich phenolics in brown rice (BR). Our previous study showed that hydrogen gas (H₂) promoted both germination and phenolic accumulation in germinated brown rice (GBR), yet the underlying regulatory mechanisms remain elusive. In the present study, we demonstrated that hydrogen-rich water (HRW) treatment significantly increased the content of p-coumaric acid and ferulic acid. Integrating RNA-seq and ATAC-seq, we revealed that HRW treatment remodeled chromatin accessibility and activated genes involved in phenolic biosynthesis, mitochondrial function, and redox homeostasis. Specifically, H2 enhanced mitochondrial cristae density, modulated respiratory complexes IV activities, and induced a controlled oxidative shift via promoting ROS (O₂- and H₂O₂) generation and activating antioxidant defenses system. Consequently, key enzymes (PAL and MDH) were stimulated, enhancing TCA cycle-derived intermediates (such as malic acid) and the supply of phenylalanine as a phenolic precursor. Notably, H2 upregulated the transcription factor OsMYB4, which directly binds to the promoters of GPX and MDH expression to enhance TCA cycle flux and ROS scavenging, respectively. Collectively, our findings uncover a dual pro-oxidant and antioxidant role of H2, which orchestrates chromatin remodeling, mitochondrial metabolism, and secondary metabolite synthesis to maintain cellular homeostasis during germination. This study provides a mechanistic framework for leveraging H₂ technology in germinated cereal processing.