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Series GSE167484 Query DataSets for GSE167484
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
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.
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.
Contributor(s) Oberlin S, Rajendran R, Trasser M, Schott G, Barragán-Borrero V, Marí-Ordóñez A, Voinnet O
Citation(s) 34931432
Submission date Feb 24, 2021
Last update date Mar 30, 2022
Contact name Stefan Oberlin
Organization name ETH Zürich
Department Department of Biology
Street address Universitätstrasse 2
City Zürich
ZIP/Postal code 8092
Country Switzerland
Platforms (1)
GPL17639 Illumina HiSeq 2500 (Arabidopsis thaliana)
Samples (16)
GSM5106022 35S.EVD.Col-0 RIBO-seq
GSM5106023 35S.EVD.rdr6 RIBO-seq
GSM5106024 35S.GFP-EVD-GUS.Col-0 RIBO-seq
BioProject PRJNA704712
SRA SRP308027

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

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
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