Two transcription factors play critical roles in mediating epigenetic regulation of fruit ripening in tomato

DNA methylation regulates fruit ripening in tomato, and disruption of the DNA demethylase DEMETER-LIKE 2 (DML2) results in genome-wide DNA hypermethylation and impaired ripening. We report here that the transcription factors Ripening Inhibitor (RIN) and FRUITFULL 1 (FUL1) play critical roles in mediating the effect of DNA methylation on tomato fruit ripening. <i>RIN</i> and <i>FUL1</i> are silenced in <i>dml2</i> mutant plants, and the defective ripening phenotype of <i>dml2</i> is mimicked by the <i>rin/ful1</i> double mutant. Restoration of <i>RIN</i> expression in <i>dml2</i> partially rescues its ripening defects. DNA methylation controls ripening not only by regulating the expression of <i>RIN</i> and <i>FUL1</i> but also by interfering with the genomic binding of RIN. In <i>dml2</i> mutant plants, RIN cannot bind to some of its targets in vivo even though DNA methylation does not interfere with RIN binding in vitro; this inhibited binding in vivo is correlated with increased DNA methylation and histone H3 enrichment within 100 bp of the binding site. Our work uncovers the molecular mechanisms underlying DNA methylation control of fruit ripening in tomato.