Clearly compensating
Genetic compensation by transcriptional adaptation is a process whereby knocking out a gene (e.g by CRISPR or TALEN) results in the deregulation of genes that make up for the loss of gene function.
Pooling only 4 siRNAs increases off-target effects
Low-complexity pools (with 4 siRNAs per gene) should thus lead to overall stronger off-target effects than single siRNAs.
Citations of our Nucleic Acids Research Paper
Our 2014 Nucleic Acids Research paper provides an excellent overview of the siPOOL technology. Google Scholar shows that our paper has been cited 64 times.
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).
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.
Novel anti-cancer mechanism identified by shRNA/siRNA off-target effects
Unveiling a novel anti-cancer mechanism via siRNA/shRNA off-target effects. Putzbach et al.'s study exposes survival genes in cancer cells, shedding light on CD95/CD95L-induced cell death and the role of miRNA-like activity in off-target effects
Little correlation between Dharmacon siGENOME and ON-TARGETplus reagents
Analysis reveals little correlation between Dharmacon siGENOME and ON-TARGETplus, highlighting the complexity of validating RNAi screen hits.
Orthogonal design in software and RNAi screening
Orthogonal design in RNAi screening enhances hit confidence, contrasting with software design principles to minimize systemic interdependencies.