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| Status |
Public on Nov 24, 2014 |
| Title |
shRNA Sensor Analysis of 5' U converted shRNAs reveals 3' target bias exists in addition to 5' guide bias |
| Organism |
synthetic construct |
| Experiment type |
Other
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| Summary |
shRNAs selected with the shERWOOD algorithm were converted to have a U at the 5' end of their guide. When endogenous 1U shRNAs were compared to artificial shRNA via the sensor algorithm, the endogenous shRNAs were found to be more efficacious.
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| Overall design |
Purpose: Structural studies have hinted that the 5' end of shRNA guides is engulfed in the RISC complex. It has also been reported that shRNAs with a 5' U are more efficacious than those with other 5' caps. We wished to determine whether replacement of shRNA guide 5' nucleotides with a U, regardless of the corresponding target base, would increase their efficacy.
Method: For each gene in the "druggable genome" 10 shRNAs were selected with the shERWOOD algorithm. In each case the score was assessed as if the guide had a 5' U. Sensor constructs were designed pairing 1U-guide shRNAs with their endogenous target. shRNAs were assessed for efficacy via the shRNA sensor assay (Fellmann et al. Mol Cell 2011).
Results: shRNAs with artificial 5' Us were found to be less efficacious than those with an endogenous 5' U,
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| Contributor(s) |
Knott SR |
| Citation(s) |
25435137 |
| |
| Submission date |
Oct 08, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Simon Robert Vincent Knott |
| Organization name |
Cold Spring Harbor Laboratory
|
| Department |
Biology
|
| Lab |
Hannon
|
| Street address |
1 Bungtown Rd
|
| City |
Cold Spring Harbor |
| State/province |
NY |
| ZIP/Postal code |
11724 |
| Country |
USA |
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| Platforms (1) |
| GPL15228 |
Illumina HiSeq 2000 (synthetic construct) |
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| Samples (11)
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| This SubSeries is part of SuperSeries: |
| GSE62189 |
A computational algorithm to predict shRNA potency |
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| Relations |
| BioProject |
PRJNA263391 |
| SRA |
SRP048754 |
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