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| Status |
Public on Nov 14, 2016 |
| Title |
Endogenous small RNAs from Arabidopsis thaliana wild-type, dcl4 mutant and dcl4 mutant expressing nuclear or cytoplasmic DCL4 |
| Organism |
Arabidopsis thaliana |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
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| Summary |
Parallel RNA silencing pathways regulate gene expression in plants, either by transcriptional gene silencing via RNA-dependent DNA methylation (RdDM), or by post-transcriptional silencing targeting mRNAs. Both pathways rely on distinct Dicer-like proteins to cleave double-stranded RNA into small-interfering RNAs. Experiments to determine the subcellular localization of Dicer-like proteins in Arabidopsis revealed that DCL4 is predominantly expressed as a transcriptional start site isoform that encodes a cytoplasmic protein. A second, longer DCL4 transcript isoform encodes a nuclear-localization signal and its expression is repressed by DNA methylation. Consequently this isoform is induced when promoter methylation decreases due to infection with a bacterial pathogen or during silique development. Nuclear DCL4 produces unique populations of small RNAs, called DCL4NLS isoform-dependent siRNAs (disiRNAs), which function via a post-transcriptional silencing effector, but whose precursors are generated by the RdDM pathway. Arabidopsis cells can thus respond to genome methylation changes by modulating DCL4 localization, which in turn recruits PTGS factors to reinforce RNA silencing.
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| Overall design |
4 samples examined: wild type, dcl4 mutant and dcl4 mutant expressing nuclear or cytosplasmic DCL4
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| Contributor(s) |
Pumplin N, Sarazin A, Jullien PE, Bologna N, Oberlin S, Voinnet O |
| Citation(s) |
27956586 |
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| Submission date |
Nov 05, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Alexis Sarazin |
| E-mail(s) |
alexis.sarazin@biol.ethz.ch
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| Organization name |
ETH
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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 (4)
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| Relations |
| BioProject |
PRJNA301359 |
| SRA |
SRP065858 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE74731_RAW.tar |
50.0 Mb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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