Abiotic stress-induced DNA methylation in transposable elements and their transcripts reveals a multi-layered response in Moso bamboo

This study investigated the stress-induced epigenetic changes of transposable elements (TEs), TE-derived long non-coding RNAs (TE-lncRNAs), and TE-derived circular RNA (TE-circRNAs) in Moso bamboo seedlings exposed to various abiotic stresses. Long terminal repeat (LTR) retrotransposons and terminal inverted repeat (TIR) transposons exhibited higher levels of CG and CHG methylation within their bodies compared with their flanking regions. Ty1/copia and Ty3/gypsy retrotransposons exhibited similar methylation patterns in the LTR and coding regions. Conversely, MULE, hAT, and ENspm transposons displayed a trend of rising and then decreasing methylation patterns in the TIR regions. Stress-induced hypomethylation of coding regions enhanced the reactivation of TEs. Around 12.4% of lncRNAs and 11% of circRNAs were derived from TEs. TE-lncRNAs and TE-circRNAs were primarily derived from Ty1/copia and Ty3/gypsy superfamilies. No significant differences were observed in length distribution and expression patterns between TE-lincRNAs and non-TE-lincRNAs. In contrast, TE-circRNAs exhibited significantly higher expression levels compared with non-TE-circRNAs. TE-lncRNAs displayed stress-specific expression patterns, with tendencies for down-regulation under cold and salt stress and up-regulation under heat stress. TE-lncRNAs targeted various heat shock protein genes and heat stress transcription factor genes under heat stress condition. Gene network analysis revealed that Ph-TE-lncRNA3 and Ph-TE-circRNA3 play crucial roles in heat and UV stress response by regulating downstream genes. This study elucidates how TEs in Moso bamboo respond to stress and the role of TE-lncRNAs and TE-circRNAs in regulating stress tolerance.