Low complexity pooling does not prevent siRNA off-targets
Low-complexity siRNA pooling (e.g. Dharmacon siGENOME SMARTpools) does not prevent siRNA off-targets. It may in fact exacerbate off-target effects. Only high-complexity pooling (siPOOLs) can reliably ensure on-target phenotypes.
What is the probability of an siRNA off-target phenotype?
Conventional siRNAs have a high probability of giving off-target phenotypes. siRNA off-target effects can be reduced by using more specific reagents or narrowing the assay focus (to reduce the number of relevant genes).
5 factors to consider in multi-gene targeting RNAi screens
Effective functional genomic screening depends on a variety of factors that need to be simultaneously addressed to obtain meaningful results. A recent Cell Reports paper demonstrates this by taking a holistic approach to siRNA screening with the use of multi-isoform/multi-gene targeting to address redundant paralogs and pathways in cancer cells.
Is it important to avoid microRNA binding sites during siRNA design?
To address the question of whether one should avoid microRNA binding sites during siRNA design, we examined whether removing siRNAs that share seeds with native microRNAs would reduce the dominance of seed-based off-target effects in RNAi screening.
Correcting seed-based off-target effects in RNAi screens
Unlocking RNAi screening potential by correcting seed-based off-target effects. While seed correction methods yield minor improvements, challenges persist in interpreting strongest hits. The quest for precise reagents, like high-complexity siPOOLs, remains crucial for reliable results.
Making sense of siGENOME deconvolution
Deconvolution of Dharmacon siGENOME pools shows surprising results, with low correlation to target genes and significant seed effects.
The final RNAiL?
Explore the debate over RNAi's viability post-CRISPR revelations. Lin et al.'s findings challenge RNAi's efficacy, but nuances suggest RNAi still has value, albeit with precautions against off-target effects
Where's the beef?
Uncover the impact of on- vs. off-target effects in RNAi screening. Analysis of Hasson et al.'s genome-wide screen reveals the prevalence of off-target effects, emphasizing the need for precise siRNA libraries.
Classic Papers Series: Lin et al. show RNAi screen dominated by seed effects
Classic Papers Series: Lin et al. show RNAi screen dominated by seed effects Classic Papers Series: Lin et al. show RNAi screen dominated...
The nasty, ugly fact of off-target effects
Discover the fascinating history of siRNAs and their impact on gene targeting. Explore the disappointments and lessons learned from siRNA screening.