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| Status |
Public on Apr 09, 2018 |
| Title |
Comprehensive Analysis of RDR1/2/6-independent Small RNAs in Arabidopsis thaliana |
| Organism |
Arabidopsis thaliana |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
Plant small RNAs (sRNAs) regulate key physiological mechanisms through post-transcriptional and transcriptional silencing of gene expression. sRNAs fall into two major categories: those that are reliant on RNA Dependent RNA Polymerases (RDRs) for biogenesis and those that aren’t. Known RDR-dependent sRNAs include phased and repeat-associated short interfering RNAs, while known RDR-independent sRNAs are primarily microRNAs (miRNAs) and other hairpin-derived sRNAs. In this study, we produced and analyzed sRNA-seq libraries produced from rdr1/rdr2/rdr6 triple mutant plants. We found 58 previously annotated MIRNA loci that were dependent on RDR function, casting doubt on their classification as MIRNAs. We also found 38 RDR-independent sRNA clusters that were not MIRNAs or otherwise hairpin-derived. These 38 sRNA loci have novel biogenesis mechanisms, and frequently arise from protein-coding genes. Altogether, our analysis suggests that these 38 sRNA loci represent one or more new types of sRNA loci in Arabidopsis thaliana.
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| Overall design |
Small RNA sequencing from Arabidopsis thaliana wild-type (Col-0 ecotype) and rdr1-1/rdr2-1/rdr6-15 triple mutant inflorescences
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| Contributor(s) |
Polydore S, Coruh C, Axtell MJ |
| Citation |
Seth Polydore, Michael Axtell. Analysis of RDR1/RDR2/RDR6-independent small RNAs in Arabidopsis thaliana improves MIRNA annotations and reveals novel siRNA loci. bioRxiv 238691; doi:10.1101/238691
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| |
| Submission date |
Oct 19, 2017 |
| Last update date |
Jul 25, 2021 |
| Contact name |
Michael J Axtell |
| E-mail(s) |
mja18@psu.edu
|
| Organization name |
Pennsylvania State University
|
| Department |
Biology
|
| Lab |
Axtell
|
| Street address |
280 Mueller Lab
|
| City |
University Park |
| State/province |
PA |
| ZIP/Postal code |
16802 |
| Country |
USA |
| |
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| Platforms (1) |
| GPL17639 |
Illumina HiSeq 2500 (Arabidopsis thaliana) |
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| Samples (6)
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| Relations |
| BioProject |
PRJNA415084 |
| SRA |
SRP120564 |
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