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| Status |
Public on Jun 12, 2013 |
| Title |
Multiple RNA recognition patterns during microRNA biogenesis in plants |
| Organism |
Arabidopsis thaliana |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
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| Summary |
MicroRNAs (miRNAs) are processed from longer precursors with fold-back structures. While animal MIRNA precursors have homogenous structures, plant precursors comprise a collection of fold-backs with variable size and shape. Here, we design an approach (SPARE) to systematically analyze miRNA processing intermediates and characterize the biogenesis of most of the evolutionary conserved miRNAs present in Arabidopsis thaliana. We found that plant MIRNAs are processed by four mechanisms, depending on the sequential direction of the processing machinery and the number of cuts required to release the miRNA. Classification of the precursors according to their processing mechanism revealed specific structural determinants for each group. We found that the complexity of the miRNA processing pathways occurs in both ancient and evolutionary young sequences, and that members of the same family can be processed in different ways. We observed that different structural determinants compete for the processing machinery and that alternative miRNAs can be generated from a single precursor. The results provide a mechanistic explanation for the structural diversity of MIRNA precursors in plants and new insights towards the understanding of the biogenesis of small RNAs.
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| Overall design |
Approach to systematically analyze miRNA processing intermediates and characterize the biogenesis of conserved and young miRNAs present in Arabidopsis thaliana. MiRNA processing intermediates profiles of Wild type and Fiery mutants Arabidopsis plants were analyzed, using Illumina GAIIx.
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| Contributor(s) |
Bologna NG, Schapire AL, Zhai J, Chorostecki U, Boisbouvier J, Meyers BC, Palatnik JF |
| Citation(s) |
23990609 |
| Submission date |
Apr 26, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Uciel Pablo Chorostecki |
| Organization name |
IBR
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| Street address |
Ocampo y Esmeralda
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| City |
Rosario |
| ZIP/Postal code |
2000 |
| Country |
Argentina |
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| Platforms (1) |
| GPL9302 |
Illumina Genome Analyzer II (Arabidopsis thaliana) |
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| Samples (2) |
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| Relations |
| BioProject |
PRJNA200315 |
| SRA |
SRP021538 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE46429_RAW.tar |
30.0 Kb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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