DNA hypomethylation enables the transcriptional repressor SlSPL-CNR to control fruit flavor ester biosynthesis

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.