LncRNA asCsMTP6-CsMTP6 module regulates mitochondrial manganese homeostasis in cucumber

High concentrations of manganese (Mn) ions in the soil of facility-based cultivation significantly restrict the development of the cucumber industry. However, the genetic mechanisms governing Mn accumulation in crops are still not well comprehended. Through the comprehensive integration of molecular biology, epigenetic modification analysis combined with genetic analysis, we functionally characterized a novel regulatory module. Consisting of a long non-coding RNA (lncRNA, asCsMTP6) and its mitochondria-localized target Metal Tolerance Protein 6 (MTP6), it coordinately regulates Mn accumulation in cucumber. CRISPR-CsMTP6 or asCsMTP6-OE mimics toxicity, whereas CsMTP6-OE or asCsMTP6 knockdown enhances tolerance, confirming that asCsMTP6 negatively regulates CsMTP6 transcription. Additionally, the H3K27me3 methylation marks surrounding the CsMTP6 genome are reduced under Mn stress, and the inhibited expression of asCsMTP6 results in a lower level of H3K27me3 methylation in the CsMTP6 gene body and 3'UTR region, thereby facilitating the expression of CsMTP6 for tolerance to Mn stress. Furthermore, virus-induced silencing of histone methyltransferases SWN and CLF also reduces H3K27me3 methylation in the CsMTP6 genomic region, thus releasing the expression of CsMTP6. Taken together, this study demonstrates the epigenetic regulation of lncRNAs in response to Mn stress, providing new insights into the potential for developing cucumber varieties with improved tolerance to manganese-contaminated soils.