A RIN ‐ SlJMJ6 transcriptional–epigenetic module activates carotenoid biosynthesis through H3K27me3 demethylation in tomato

Fruit ripening involves extensive transcriptional and epigenetic reprogramming, yet how chromatin modifiers are targeted to specific genomic loci in coordination with transcription factors remains unclear. Here, we show that the histone H3K27me3 demethylase SlJMJ6 physically and functionally associates with the master ripening regulator RIPENING INHIBITOR (RIN) to regulate carotenoid biosynthesis in tomato (Solanum lycopersicum) fruit. Genetic and transcriptional analyses demonstrated that SlJMJ6 and RIN cooperatively promote carotenoid accumulation and activate key biosynthetic genes, including PSY1, DXS1 and ZISO. Genome-wide analyses revealed that SlJMJ6 preferentially binds promoter regions enriched in CArG motifs and extensively co-occupies ripening-associated genes with RIN. Epigenomic analyses showed that SlJMJ6 association correlates with reduced H3K27me3 enrichment at co-targeted loci, whereas loss of either SlJMJ6 or RIN increases H3K27me3 enrichment and reduces expression of ripening-related genes. Furthermore, SlJMJ6 occupancy at representative target loci is markedly reduced in the rin mutant, indicating that RIN facilitates SlJMJ6 chromatin association. Together, our findings reveal a cooperative RIN-SlJMJ6 regulatory module linking RIN-dependent transcriptional regulation with locus-specific H3K27me3 dynamics, providing a mechanistic framework for chromatin-mediated activation of metabolic genes during fruit ripening.