4‑AllylanisolePromotes the Root Growth of Arabidopsis thaliana by Inhibiting AtHDA9 Activity

This study elucidates the epigenetic mechanism through which 4-allylanisole, a key monoterpene in Foeniculum vulgare essential oils, regulates plant growth. Integrated RNA-Seq and ChIP-Seq analyses revealed 4-allylanisole enhances histone H3K9 acetylation (H3K9ac) at promoters of growth-related genes in Arabidopsis thaliana, concomitant with improved root development and biomass accumulation. Biochemical assays identified AtHDA9 histone deacetylase as the molecular target, showing 4-allylanisole directly inhibits its enzymatic activity through stable interactions with catalytic residues (Asp95, Phe202, Leu268, His174) confirmed by molecular docking and dynamics simulations. The suppressed deacetylation elevated endogenous indole-3-acetic acid (IAA) levels and amplified auxin signaling transduction. These findings establish a dual mechanism whereby 4-allylanisole epigenetically activates growth-related gene expression through H3K9ac accumulation while coordinately enhancing IAA biosynthesis and signaling. This work provides the first evidence of plant-derived volatile compounds regulating growth through histone modification-auxin crosstalk, proposing novel strategies for developing eco-friendly plant growth regulators.