|
| Status |
Public on Jun 05, 2013 |
| Title |
Sequence analysis of scnRNAs |
| Organism |
Tetrahymena thermophila |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
|
| Summary |
The developmentally regulated 26- to 32-nt siRNAs (scnRNAs) are loaded to the Argonaute protein Twi1p and display a strong bias for uracil at the 5' end. In this study, we used deep sequencing to analyze loaded and unloaded populations of scnRNAs. We show that the size of the scnRNA is determined during a pre-loading process, whereas their 5' uracil bias is attributed to both pre-loading and loading processes. We also demonstrate that scnRNAs have a strong bias for adenine at the third base from the 3' terminus, suggesting that most scnRNAs are direct Dicer products. Furthermore, we show that the thermodynamic asymmetry of the scnRNA duplex does not affect the guide and passenger strand decision. Finally, we show that scnRNAs frequently have templated uracil at the last base without a strong bias for adenine at the second base indicating non-sequential production of scnRNAs from substrates. These findings provide a biochemical basis for the varying attributes of scnRNAs, which should help improve our understanding of the production and turnover of scnRNAs in vivo.
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| |
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| Overall design |
We compared Twi1p-loaded scnRNAs to scnRNAs before they have been loaded into Twi1p by deep sequencing to understand how the two processes, the production of siRNAs by Dicer and the loading of siRNAs into Argonaute, shape the population of siRNAs in vivo.
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| |
|
| Contributor(s) |
Mochizuki K, Kurth HM |
| Citation(s) |
23770361 |
| |
| Submission date |
Jun 05, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Kazufumi Mochizuki |
| E-mail(s) |
kazufumi.mochizuki@igh.cnrs.fr
|
| Organization name |
Institute of Human Genetics, CNRS
|
| Street address |
141 rue de la Cardonille
|
| City |
Montpellier |
| ZIP/Postal code |
34090 |
| Country |
France |
| |
|
| Platforms (2) |
| GPL15706 |
Illumina HiSeq 2000 (Tetrahymena thermophila) |
| GPL17243 |
Illumina Genome Analyzer II (Tetrahymena thermophila) |
|
| Samples (4)
|
| GSM1154017 |
scnRNAs co-immunoprecipitated with Twi1p |
| GSM1154018 |
total scnRNAs from TWI1 KO cells |
| GSM1154019 |
scnRNAs co-immunoprecipitated with HA-Twi1p |
| GSM1154020 |
scnRNAs co-immunoprecipitated with HA-Twi1p-hAGO2Lmut |
|
| Relations |
| BioProject |
PRJNA207031 |
| SRA |
SRP024243 |
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