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| Status |
Public on Nov 19, 2018 |
| Title |
Plant Extracellular Vesicles Contain Diverse Small RNA Species and Are Enriched in 10 to 17 Nucleotide "Tiny" RNAs. |
| Organism |
Arabidopsis thaliana |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
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| Summary |
Small RNAs (sRNAs) are small non-coding RNAs of 20 to 24 nucleotides in size found across a wide range of eukaryote organisms, from plants to animals. sRNAs are master regulators of a wide range of biological functions, including development, reproduction and stress responses. They typically function via the control of the stability and translation of target mRNAs. sRNAs can be divided in two major classes, according to their biogenesis and mode of action: microRNAs (miRNAs) and small interfering RNAs (siRNAs). As a silencing signal, several different types of sRNAs have also the ability to move short distances, like cell-to-cell, or much longer distances like root to shoot. They are even trafficked between different species and organisms. However, the mechanisms by which sRNAs move remain unknown. Extracellular vesicles (EVs) are mobile lipid compartments that participate in intercellular communication; they are able to carry proteins, lipids, nucleic acids and metabolites. Despite the fact that very little is known about the origin, formation or function of EVs in plants, recent results suggest that they participate in both long distance movement and immune responses. In this study, we analysed the small RNA content of EVs, and we identified miRNAs and siRNAs that are preferentially loaded into the EVs. This EV enrichment of certain RNAs supports hypotheses for long-distance RNA movement and for RNA-based communication between species, including host-pathogen interactions.
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| Overall design |
[Col-0] 3 different biological replicates of small RNA seq from Arabidopsis leaf total RNA, Extracellular vesicles and supernatant are included in this study.
[dcl234 triple mutant] 2 different biological replicates of small RNA seq from dcl234 triple mutant Arabidopsis leaf total RNA, Extracellular vesicles and supernatant are included in this study.
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| Contributor(s) |
Baldrich P, Rutter BD, Podicheti R, Innes RW, Meyers BC |
| Citation(s) |
30705133 |
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| Submission date |
May 21, 2018 |
| Last update date |
Mar 19, 2019 |
| Contact name |
Patricia Baldrich Gonzalez |
| E-mail(s) |
pbaldrich@ucdavis.edu
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| Organization name |
University of California - Davis
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| Department |
Genome Center
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| Lab |
Meyers Lab
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| Street address |
451 Health Sciences Dr., Davis, CA 95616
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| City |
Davis |
| State/province |
CA |
| ZIP/Postal code |
95616 |
| Country |
USA |
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| Platforms (1) |
| GPL19580 |
Illumina NextSeq 500 (Arabidopsis thaliana) |
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| Samples (15)
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| GSM3147539 |
Supernatant RNA, Col-0, Replicate 1 |
| GSM3147540 |
Supernatant RNA, Col-0, Replicate 2 |
| GSM3147541 |
Supernatant RNA, Col-0, Replicate 3 |
| GSM3147542 |
EV RNA, Col-0, Replicate 1 |
| GSM3147543 |
EV RNA, Col-0, Replicate 2 |
| GSM3147544 |
EV RNA, Col-0, Replicate 3 |
| GSM3377800 |
Leaf TotalRNA, dcl234 triple mutant, Replicate 1 |
| GSM3377801 |
Leaf TotalRNA, dcl234 triple mutant, Replicate 2 |
| GSM3377802 |
Supernatant RNA, dcl234 triple mutant, Replicate 1 |
| GSM3377803 |
Supernatant RNA, dcl234 triple mutant, Replicate 2 |
| GSM3377804 |
EV RNA, dcl234 triple mutant, Replicate 1 |
| GSM3377805 |
EV RNA, dcl234 triple mutant, Replicate 2 |
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| Relations |
| BioProject |
PRJNA472309 |
| SRA |
SRP148558 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE114696_RAW.tar |
420.9 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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