GEOapplication/xmlftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE329nnn/GSE329250/primary200OKGenomicsSolanum lycopersicumGenome binding/occupancy profiling by high throughput sequencinghttps://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE329250GEOGSEfalseDNA hypomethylation enables the transcriptional repressor SlSPL-CNR to control fruit flavor ester biosynthesisDNA hypomethylation is traditionally associated with gene activation. Here we show that DNA hypomethylation permits the binding of a transcriptional repressor SlSPL-CNR, leading to gene silencing in tomato. SlSPL-CNR exhibits methylation-sensitive DNA binding and preferentially occupies unmethylated GTACGG motifs. During fruit ripening, SlDML2-mediated DNA demethylation at the SlAAT1 promoter allows SlSPL-CNR binding, which represses SlAAT1 expression and modulates the biosynthesis of fruit flavor esters. Structural analysis reveals that cytosine methylation introduces a steric clash with Gln94 in the SBP domain. CRISPR knockout of SlSPL-CNR de-represses SlAAT1 and increases ester accumulation. This methylation-sensitive binding is conserved across SBP domain proteins from rice, maize, and tomato. Our findings reveal a mechanism where DNA hypomethylation facilitates repressor recruitment, linking epigenetic dynamics to metabolic control in plants.2026/06/18GSE329250329250Solanum lycopersicum