RNA–protein interactions reveals the pivotal role of lncRNA1840 in tomato fruit maturation

SUMMARY Long non‐coding RNAs (lncRNAs) play crucial roles in various biological processes in plants. However, the functional mechanism of lncRNAs in fruit ripening, particularly the transition from unripe to ripe stages, remains elusive. One such lncRNA1840, reported by our group, was found to have important role in tomato fruit ripening. In the present study, we gain insight into its functional role in fruit ripening. CRISPR‐Cas9 mediated lncRNA1840 mutants caused the delayed tomato fruit ripening. Notably, loss function of lncRNA1840 did not directly impact ethylene signaling but rather delay ethylene synthesis. Transcriptomic analysis revealed differences in the expression of ripening related genes in lncRNA1840 mutants, suggesting that it is involved in gene regulation of fruit ripening. We used Chromatin Isolation by RNA Purification (ChIRP)‐Seq to identify lncRNA1840 binding sites on chromatin. ChIRP‐seq suggested that lncRNA1840 had occupancy on 40 genes, but none of them is differentially expressed genes in transcriptomic analysis, which indicated lncRNA1840 might indirectly modulate the gene expression. ChIRP‐mass spectrometry analysis identified potential protein interactors of lncRNA1840, Pre‐mRNA processing splicing factor 8, highlighting its involvement in post‐transcriptional regulatory pathways. In summary, lncRNA1840 is key player in tomato plant growth and fruit ripening, with multifaceted roles in gene expression and regulatory networks. Significance Statement Long non‐coding RNAs (lncRNAs) play important roles in various biological processes in plants, but the mechanism of action of lncRNAs during fruit ripening remains unexplored. lncRNA1840 was identified in tomato, which confirmed that it affected the ripening process of tomato fruit and achieved post‐transcriptional regulation by participating in alternative splicing, which improved the regulatory network of tomato fruit ripening and filled the gap of lncRNA in the field of fruit ripening.