Synergism between SCT1/SCT2 and DNA methylation regulates the expression of Copia2 retrotransposon in rice

Transposable elements (TEs) are essential constituents of plant genomes, promoting environmental adaptation and modulating gene expression through novel insertions. Although their activities can also trigger deleterious mutations, host mechanisms have evolved to repress them. Similarly, TEs have developed strategies to counteract silencing for their propagation. Here, the LTR retrotransposon Copia2 was identified as an active TE in japonica rice, with variations in 5-base-pair repeats within its 5'-LTR influencing promoter activity. The expression of Copia2 could be activated by drought conditions, with CG-1 motifs on LTR acting as cis-acting elements recognized by calmodulin-binding transcription activators. Under drought stress, the interaction of drought-induced proteins SCT1 and SCT2 with calmodulin OsCML4 and OsCML31 further activates Copia2 expression, enhancing its sensitivity to Ca²⁺ signaling. Additionally, decreased DNA methylation of Copia2 under drought conditions, regulated by Ca²⁺ signaling, facilitates the binding of SCT1 and SCT2 to the LTR. In summary, the drought-induced activity of Copia2 is regulated by the synergy of SCT1/SCT2 and DNA methylation mediated through Ca²⁺ signaling, potentially contributing to its recent activity in rice.