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• A rice Zeta family glutathione-S-transferase (OsGSTZ4) gene for Cd detoxification was investigated. • Heterologous expression of OsGSTZ4 in a yeast conferred cellular Cd tolerance. • CHH hypermethylation at a MITE transposable element was found to be inserted in the 5′-untranscribed region of OsGSTZ4. • Three 24-nt siRNAs derived from the TE were detected and was rapidly enriched under Cd stress. • This study helps understand the diversity of gene regulation via an epigenetic mechanism for rice adaptation to the environmental stress. Environmental contaminants such as cadmium (Cd) pose high risks to crop production and human health. The genetic basis for regulation of Cd stress-responsive genes for plant adaptation to adverse environments remains poorly understood. In this study, we characterized a rice Zeta family glutathione-S-transferase (OsGSTZ4) gene for Cd detoxification. Heterologous expression of OsGSTZ4 in a yeast (Saccharomyces cerevisiae) conferred cellular Cd tolerance. Transgenic rice overexpressing OsGSTZ4 improved plant growth, attenuated Cd-induced toxicity, and accumulated more Cd in roots. OsGSTZ4 transcription was rapidly induced 3 h after Cd exposure and then declined to the basal level. This was followed by (days after Cd treatment) by CHH hypermethylation (by 41.2 %) at a MITE (Miniature Inverted-repeat Transposable Element) transposable element (TE) inserted in the 5′-untranscribed region (UTR) (-1,722 ∼ -1,392 bp) of OsGSTZ4. Meanwhile, three 24-nt siRNAs derived from the TE (-1,722 ∼ -1,471 bp) were detected and was also rapidly enriched under Cd stress. To validate the possibility that Cd-induced change in OsGSTZ4 expression correlates with the siRNAs-involved CHH methylation through an RdDM (RNA-directed DNA methylation) pathway, genetic analyses were performed. We found that the CHH methylation at the promoter and transcript level of OsGSTZ4 were compromised in the osdrm2 (loss of function for CHH methylation) and osrdr2i (defective in RNA-dependent RNA polymerase 2) but did not change in other types of methyltransferases such as osmet1, ossdg714 or osros1. Promoter deletion analyses confirmed that the siRNA target sequences were essential for the proper expression of OsGSTZ4. Our studies reveal an unusual feedback mechanism by which the Cd-induced rapid OsGSTZ4 expression for Cd tolerance would interplay with the late CHH hypermethylation to silence the TE through the 24-nt siRNAs- and Osdrm2-mediated RdDM pathway, and help understand the diversity of gene regulation via an epigenetic mechanism for rice adaptation to the environmental stress. [ABSTRACT FROM AUTHOR]