Oberlin et al. 2021 (PRJNA704712)

General Details

Title Innate, translation-dependent silencing of an invasive transposon in Arabidopsis
Organism
Number of Samples 4
Release Date 2021/02/24 00:00
Sequencing Types
Protocol Details

Study Links

Repository Details

SRA SRP308027
ENA SRP308027
GEO
BioProject PRJNA704712

Publication

Title
Authors Oberlin S,Rajeswaran R,Trasser M,Barragán-Borrero V,Schon MA,Plotnikova A,Loncsek L,Nodine MD,Marí-Ordóñez A,Voinnet O
Journal EMBO reports
Publication Date 2022 Feb 3
Abstract 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. © 2021 The Authors. Published under the terms of the CC BY 4.0 license.
PMC PMC8892269
PMID 34931432
DOI
Run Accession Study Accession Scientific Name Cell Line Library Type Treatment GWIPS-viz Trips-Viz Reads BAM BigWig (F) BigWig (R)
SRR13780863 PRJNA704712 Arabidopsis thaliana Ribo-Seq
SRR13780864 PRJNA704712 Arabidopsis thaliana Ribo-Seq
SRR13780865 PRJNA704712 Arabidopsis thaliana Ribo-Seq
SRR13780866 PRJNA704712 Arabidopsis thaliana Ribo-Seq
Run Accession Study Accession Scientific Name Cell Line Library Type Treatment GWIPS-viz Trips-Viz Reads BAM BigWig (F) BigWig (R)

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