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| Status |
Public on Feb 23, 2017 |
| Title |
tRNA-derived small RNAs target transposable element transcripts |
| Organism |
Arabidopsis thaliana |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
Other
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| Summary |
Background: Eukaryotic organisms have evolved a series of mechanisms to regulate transposable element (TE) expression based on RNA silencing. In plants, the initial step in the recognition of TE transcripts relies on microRNAs, but this is unlikely to take place in the pollen grain where natural reactivation of TE transcription occurs but microRNAs accumulate to low levels. We investigated small non-coding RNA accumulation in plants and found conserved tRNA-derived RNA fragment (tRF) accumulation in the pollen grain or analogous reproductive structure in a variety of plant species.
Results:Analysis of tRF biology in Arabidopsis revealed that tRFs are regulated by the chromatin modifier DDM1, have a microRNA-like biogenesis pathway, and specifically target TE mRNAs. In addition, we provide evidence that tRF targeting is involved in the production of secondary small RNAs derived from TE transcripts, which initiate a cascade of RNAi and TE silencing.
Conclusion:that tRFs are bona-fide regulatory microRNA-like small RNAs involved in the regulation of genome stability through the targeting of TE transcripts.
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| Overall design |
Examination of pollen and flower bud small RNAs from wild type, single or double mutant combinations, many of which have biological replicates. In addition, IP purificaton of the AGO1 protein followed by sequencing of the incorporated small RNAs.
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| Contributor(s) |
Slotkin RK, Martinez-Arias GE |
| Citation(s) |
28335016 |
| Submission date |
Dec 04, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
German Martinez |
| E-mail(s) |
german.martinez.arias@slu.se
|
| Organization name |
Swedish University of Agricultural Sciences
|
| Department |
Plant Biology
|
| Lab |
Martinez Lab
|
| Street address |
Almas Allé 8
|
| City |
Uppsala |
| State/province |
Uppsala |
| ZIP/Postal code |
750 07 |
| Country |
Sweden |
| |
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| Platforms (2) |
| GPL13222 |
Illumina HiSeq 2000 (Arabidopsis thaliana) |
| GPL17639 |
Illumina HiSeq 2500 (Arabidopsis thaliana) |
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| Samples (11)
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| Relations |
| BioProject |
PRJNA269310 |
| SRA |
SRP050570 |
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