Poster Presentations
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Universal features for predicting the silencing efficiency of siRNAs and shRNAs
Svetlana Shabalina, , National Institute Of Health
Small interfering (si)RNAs and small hairpin (sh)RNAs have become important tools for cell and molecular biology[1-3]. Reliable design of these molecules is essential for the needs of large functional genomics projects. To improve prediction of the silencing efficiency of small RNAs, we performed comparative, thermodynamic and correlation analyses of heterogeneous sets of several thousand siRNAs and miR30-based shRNAs. We used a non-overlapping cross-validation technique in order to select reliable structural features and optimize computational models for each dataset. We identified parameters that correlate with silencing efficiency and optimized thermodynamic features of the siRNA and shRNA antisense strands. Significantly preferred and avoided nucleotides at all sequence positions were evaluated by correlation and t-test analyses of the siRNA and shRNA training sets. The position-dependent preferences showed stable predictive power in our models for both sets. Among other features, a thermodynamic duplex stability and position-dependent thermodynamic profile (dinucleotide free energy) added predictive power to the models. We identified universal features and optimized parameters for predicting the silencing efficiency of both siRNAs and shRNAs. Incorporation of siRNA-specific and shRNA-specific parameters improved prediction results meaningfully for these molecules. Using optimized prediction models, we performed a transcriptome-wide analysis of optimal siRNA and shRNA human targets.
Endoribonuclease-prepared siRNA (esiRNA) Libraries for Loss-of-function Studies of Human and Mouse Long Non-coding RNAs
Mirko Theis, CSO, Eupheria Biotech GmbH
Long non-coding RNAs (lncRNAs) are involved in a broad spectrum of biological processes. Regardless of their important role, the tools to study lncRNA functions in cellular systems remain scarce. Here, we describe a library of endoribonuclease-prepared siRNAs (esiRNAs) for human and mouse long non-coding RNAs. esiRNAs have proven to be potent and specific mediators of RNA interference and are well-established for the silencing of coding transcripts. We extended this technology to the silencing of lncRNAs proving esiRNA effectiveness. The enhanced performance of esiRNAs in comparison to individual siRNAs is based on the pooling of many siRNA-like molecules, which are all directed against the same target-transcript. Pooling improves the specificity by largely decreasing off-target effects. Because esiRNAs are complex mixtures of several hundreds of siRNAs they also abolish the labor intense search for efficient individual siRNAs. These and other features make esiRNA a well suited instrument to study non-coding RNA function.
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