Innate, translation‐dependent silencing of an invasive transposon in Arabidopsis

Co‐evolution between hosts’ and parasites’ genomes shapes diverse pathways of acquired immunity based on silencing small (s)RNAs. In plants, sRNAs cause heterochromatinization, sequence degeneration, and, ultimately, loss of autonomy of most transposable elements (TEs). Recognition of newly invasive plant TEs, by contrast, involves an innate antiviral‐like silencing response. To investigate this response’s activation, we studied the single‐copy element EVADÉ ( EVD ), one of few representatives of the large Ty1/Copia family able to proliferate in Arabidopsis when epigenetically reactivated. In Ty1/Copia elements, a short subgenomic mRNA ( shGAG ) provides the necessary excess of structural GAG protein over the catalytic components encoded by the full‐length genomic flGAG‐POL . We show here that the predominant cytosolic distribution of shGAG strongly favors its translation over mostly nuclear flGAG‐POL . During this process, an unusually intense ribosomal stalling event coincides with mRNA breakage yielding unconventional 5’OH RNA fragments that evade RNA quality control. The starting point of sRNA production by RNA‐DEPENDENT‐RNA‐POLYMERASE‐6 (RDR6), exclusively on shGAG , occurs precisely at this breakage point. This hitherto ‐unrecognized “translation‐dependent silencing” (TdS) is independent of codon usage or GC content and is not observed on TE remnants populating the Arabidopsis genome, consistent with their poor association, if any, with polysomes. We propose that TdS forms a primal defense against EVD de novo invasions that underlies its associated sRNA pattern. SYNOPSIS Analyzing the initiation of RNA silencing of the Arabidopsis transposon EVADE (EVD) reveals a ribosome stalling event during EVD translation that correlates with the production of small RNAs involving RNA‐dependent RNA polymerase 6 (RDR6). Only a cytoplasmic and translated mRNA isoform of EVD triggers RDR6‐dependent siRNA production. An intense and discrete ribosome stalling event coincides with the onset of EVD siRNA production from this isoform. Atypical 5’‐OH RNA cleavage fragments overlap with the ribosome stalling site and possibly serve as RDR6 substrates. Graphical Abstract Analyzing the initiation of RNA silencing of the Arabidopsis transposon EVADE (EVD) reveals a ribosome stalling event during EVD translation that correlates with the production of small RNAs involving RNA‐dependent RNA polymerase 6 (RDR6).