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Series GSE93584 Query DataSets for GSE93584
Status Public on Jul 18, 2017
Title A genome-wide transcriptome and translatome analysis of Arabidopsis transposons identifies a unique and conserved genome expression strategy for Ty1/Copia retroelements
Organism Arabidopsis thaliana
Experiment type Expression profiling by high throughput sequencing
Non-coding RNA profiling by high throughput sequencing
Summary Retroelements, the prevalent class of plant transposons, have major impacts on host genome integrity and evolution. They produce multiple proteins from highly compact genomes and, similarly to viruses, must have evolved original strategies to optimize gene expression, although this aspect has been seldom investigated thus far. Here, we have established a high-resolution transcriptome/translatome map for the near-entirety of Arabidopsis thaliana transposons, using two distinct DNA methylation mutants in which transposon expression is broadly de-repressed. The value of this map to study potentially intact and transcriptionally active transposons in Arabidopsis thaliana is illustrated by our comprehensive analysis of the co-transcriptional and translational features of Ty1/Copia elements, a family of young and active retroelements in plant genomes, and how such features impact their biology. Genome-wide transcript profiling revealed a unique and widely conserved alternative splicing event coupled to premature termination that allows for the synthesis of a short subgenomic RNA solely dedicated to production of the Gag structural protein and preferentially associates with polysomes for efficient translation. Mutations engineered in a transgenic version of the Arabidopsis EVD Ty1/Copia element further show how alternative splicing is crucial for the appropriate coordination of full length and subgenomic RNA transcription. We propose that this hitherto undescribed genome expression strategy, conserved amongst plant Ty1/Copia elements, enables an excess of structural versus catalytic components, mandatory for mobilization.
Overall design Total RNA-seq and 3'end mRNA-seq from total RNA and polysome associated RNA in transposon derepressed backgrounds. Complementary, sRNA-seq in one background with strong transposon reactivation was generated.
Contributor(s) Oberlin S, Sarazin A, Chevalier C, Voinnet O, Marí-Ordóñez A
Citation(s) 28784835
Submission date Jan 13, 2017
Last update date May 15, 2019
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 (17)
GSM2455322 TruSeq Col-0 Rep1
GSM2455323 TruSeq Col-0 Rep2
GSM2455324 TruSeq ddm1 Rep1
BioProject PRJNA361224
SRA SRP096705

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Supplementary file Size Download File type/resource
GSE93584_QuantSeq_CPM.txt.gz 1.3 Mb (ftp)(http) TXT
GSE93584_TrueSeq_CPM.txt.gz 1.3 Mb (ftp)(http) TXT
GSE93584_met1_sRNA_processed.txt.gz 32.8 Mb (ftp)(http) TXT
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Processed data are available on Series record

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