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| Status |
Public on Aug 08, 2021 |
| Title |
Innate, translation-dependent silencing of an invasive transposon in Arabidopsis |
| Organism |
Arabidopsis thaliana |
| Experiment type |
Expression profiling by high throughput sequencing
Non-coding RNA profiling by high throughput sequencing
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| Summary |
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.
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| Overall design |
Ribo-seq and sRNA-seq were performed on RNA from inflorescence tissue of EVD and GFP-EVD-GUS overexpressing plants. NanoPare and SMART-seq2 was perfomed on wild-type (Col-0) and ddm1-2 inflorescence tissue.
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| Contributor(s) |
Oberlin S, Rajendran R, Trasser M, Schott G, Barragán-Borrero V, Marí-Ordóñez A, Voinnet O |
| Citation(s) |
34931432 |
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| Submission date |
Feb 24, 2021 |
| Last update date |
Mar 30, 2022 |
| Contact name |
Stefan Oberlin |
| E-mail(s) |
stefan.oberlin@ucsf.edu
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| Organization name |
ETH Zürich
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| Department |
Department of Biology
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| Street address |
Universitätstrasse 2
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| City |
Zürich |
| ZIP/Postal code |
8092 |
| Country |
Switzerland |
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| Platforms (1) |
| GPL17639 |
Illumina HiSeq 2500 (Arabidopsis thaliana) |
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| Samples (16)
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| Relations |
| BioProject |
PRJNA704712 |
| SRA |
SRP308027 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE167484_RiboSeq_transcript_counts.csv.gz |
10.6 Mb |
(ftp)(http) |
CSV |
| GSE167484_consensus_features.bed.gz |
397.6 Kb |
(ftp)(http) |
BED |
| GSE167484_end_feature.rpm.csv.gz |
279.1 Kb |
(ftp)(http) |
CSV |
| GSE167484_gene_TPM_SMARTseq2.csv.gz |
329.0 Kb |
(ftp)(http) |
CSV |
| GSE167484_normalized_counts_sRNA.csv.gz |
928.4 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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