RNA deadenylation pathway suppresses transposable elements in Arabidopsis

Transposable elements (TEs) are stretches of DNA that can move around the genomes and therefore are potentially detrimental to the genome stability and integrity. In plants, such danger of transposon is prevented by the epigenetic mechanisms that involve small RNA, heterochromatin formation and DNA methylation. Upon the release from epigenetic suppression, transposon is subjected to post-transcriptional repression, our knowledge of which is, however, still largely fragmental. We previously showed that transposon RNA harbors structural aberrancy owing to its inherently suboptimal codon usage and frequent cleavage. Therefore, we hypothesized that RNA decay pathways might be involved in the repression of transposon. Since the mRNA deadenylation that is mediated by the Ccr4-Not complex is the primary step of RNA decay, we tested the mutants of the Ccr4-Not complex components for transposon activity using RNA-seq, Oxford Nanopore direct RNA sequencing (ONT-DRS) and whole-genome resequencing. Intriguingly, these analyses revealed that the catalytic components of RNA deadenylase complex is required for stable repression of TEs and their mobilization by shortening the RNA tails. Our study suggests a new mechanism for transposon repression in plants that is governed by RNA deadenylation.