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SRX2488468: GSM2455323: TruSeq Col-0 Rep2; Arabidopsis thaliana; RNA-Seq
1 ILLUMINA (Illumina HiSeq 2500) run: 77.3M spots, 19.5G bases, 9.7Gb downloads

Submitted by: NCBI (GEO)
Study: A genome-wide transcriptome and translatome analysis of Arabidopsis transposons identifies a unique and conserved genome expression strategy for Ty1/Copia retroelements
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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.
Sample: TruSeq Col-0 Rep2
SAMN06227260 • SRS1918405 • All experiments • All runs
Instrument: Illumina HiSeq 2500
Strategy: RNA-Seq
Selection: cDNA
Layout: PAIRED
Construction protocol: RNA was extracted from inflorescence tissue using the TRIzol exctraction method. To generate total RNA-seq libraries, RNA was subjected to ribodepletion with Ribo Zero (Illumina) and libraries were prepared with the TruSeq Stranded mRNA Library Prep Kit (Illumina). RNA 3’end libraries were prepared using the QuantSeq 3' mRNA-Seq Library Prep Kit (Lexogen) adjusted for longer insert lengths by diluting the second strand synthesis buffer with water in a ratio 1:1.
Experiment attributes:
GEO Accession: GSM2455323
Runs: 1 run, 77.3M spots, 19.5G bases, 9.7Gb
Run# of Spots# of BasesSizePublished


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