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Summary: Transposable elements (TEs) are mobile genetic elements that can impair the host genome stability and integrity. It has been well documented that activated transposons in plants are suppressed by small interfering (si) RNAs. However, transposon repression by the cytoplasmic RNA surveillance system is unknown.Here, we show that mRNA deadenylation is critical for controlling transposons in Arabidopsis. Trimming of poly(A) tail is a rate‐limiting step that precedes the RNA decay and is primarily mediated by the CARBON CATABOLITE REPRESSION 4 (CCR4)‐NEGATIVE ON TATA‐LESS (NOT) complex.We found that the loss of CCR4a leads to strong derepression and mobilization of TEs in Arabidopsis. Intriguingly, CCR4a regulates a largely distinct set of TEs from those controlled by RNA‐dependent RNA Polymerase 6 (RDR6), a key enzyme that produces cytoplasmic siRNAs. This indicates that the cytoplasmic RNA quality control mechanism targets the TEs that are poorly recognized by the previously well‐characterized RDR6‐mediated pathway, and thereby augments the host genome stability.Our study suggests a hitherto unknown mechanism for transposon repression mediated by RNA deadenylation and unveils a complex nature of the host's strategy to maintain the genome integrity. [ABSTRACT FROM AUTHOR]

Summary Long terminal repeat retroelements (LTR‐REs) have profound effects on DNA methylation and gene regulation. Despite the vast abundance of LTR‐REs in the genome of Moso bamboo (Phyllostachys edulis), an industrial crop in underdeveloped countries, their precise implication of the LTR‐RE mobility in stress response and development remains unknown. We investigated the RNA and DNA products of LTR‐REs in Moso bamboo under various developmental stages and stressful conditions. Surprisingly, our analyses identified thousands of active LTR‐REs, particularly those located near genes involved in stress response and developmental regulation. These genes adjacent to active LTR‐REs exhibited an increased expression under stress and are associated with reduced DNA methylation that is likely affected by the induced LTR‐REs. Moreover, the analyses of simultaneous mapping of insertions and DNA methylation showed that the LTR‐REs effectively alter the epigenetic status of the genomic regions where they inserted, and concomitantly their transcriptional competence which might impact the stress resilience and growth of the host. Our work unveils the unusually strong LTR‐RE mobility in Moso bamboo and its close association with (epi)genetic changes, which supports the co‐evolution of the parasitic DNAs and host genome in attaining stress tolerance and developmental robustness. [ABSTRACT FROM AUTHOR]