Is it important to avoid microRNA binding sites during siRNA design?

Is it important to avoid microRNA binding sites during siRNA design?

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Summary: 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. siRNA design and native microRNA target sites Recently, we discussed a review of genomics screening strategies.  The authors state: RNAi screens are powerful and readily implemented discovery tools but suffer from shortcomings arising from their high levels of false negatives and false positives (OTEs) Read More

Disrupting lncRNA function with siPOOLs (RNAi), antisense oligos and CRISPR

Disrupting lncRNA function with siPOOLs (RNAi), antisense oligos and CRISPR

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Summary This blogpost covers methods used in the disruption of lncRNA function. Specifically focusing on RNA interference (with siPOOLs), antisense oligos, and CRISPR approaches. Challenges faced with these approaches are addressed. Long non-coding RNAs (lncRNAs) make up a major subgroup of RNAs and are defined as over 200 nucleotides long with limited protein-coding potential. There are three times as many genes producing lncRNAs as opposed to proteins. Numerous studies have described functional roles of lncRNAs in development and disease. This has stimulated major Read More

Correcting seed-based off-target effects in RNAi screens

Correcting seed-based off-target effects in RNAi screens

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Summary: Correcting for seed-based off-targets can improve the results from RNAi screening.  However, the correlation between siRNAs for the same gene is still poor and the strongest screening hits remain difficult to interpret. Seed-based off-target correction has little effect on reagent reproducibility Given that seed-based off-targets are the main cause of phenotypes in RNAi screening, trying to correct for those effects makes good sense. The dominance of seed-based off-targets means that independent siRNAs for the same gene usually show poor correlation. If one Read More

Little correlation between Dharmacon siGENOME and ON-TARGETplus reagents

Little correlation between Dharmacon siGENOME and ON-TARGETplus reagents

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The most common way to validate hits from Dharmacon siGENOME screens is to test the individual siRNAs from candidate pool hits (siGENOME reagents are low-complexity pools of 4 siRNAs).  In this deconvolution round, we normally see that the individual siRNAs for genes behave very differently and seed effects dominate (discussed here and here). One could argue that deconvolution is not the correct way to validate candidate hits (even though it’s the method recommended by Dharmacon),  as testing the siRNAs individually Read More

Orthogonal design in software and RNAi screening
Orthogonal design in software and RNAi screening

Orthogonal design in software and RNAi screening

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The software engineering classic The Pragmatic Progammer popularised the benefits of orthogonality in software design.  They introduce the concept by describing a decidedly non-orthogonal system: You’re on a helicopter tour of the Grand Canyon when the pilot, who made the obvious mistake of eating fish for lunch , suddenly groans and faints. Fortunately, he left you hovering 100 feet above the ground. You rationalize that the collective pitch lever [2] controls overall lift, so lowering it slightly will start a Read More

Understanding Gene Networks with Combinatorial Gene Knockdown

Understanding Gene Networks with Combinatorial Gene Knockdown

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Genes hardly ever work alone, functioning instead in complex gene networks.  Increasing advances in genomics and proteomics and corresponding developments in computational analysis, has really put this into perspective. A recent large scale RNAi study by Novartis found this hairball of a gene network in cancer cells: A gene “hairball” As such, the standard approach of disrupting the expression of a single gene to study loss-of-function phenotypes may not accurately reveal its genetic function. The highly redundant nature of signalling pathways Read More

“Phenoville” – RNAi & CRISPR Screening Strategies

“Phenoville” – RNAi & CRISPR Screening Strategies

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Pleasantville is a movie based on an interesting idea: two teenagers are magically transported through their TV to a town called Pleasantville set in the 1950s where everything is perfect (and also black-and-white).  As they discover the complex, imperfect emotions hidden below the idyllic surface, the black-and-white characters and objects start to gain colour. In loss-of-function genetic screening, some reagents and screening formats may also give rise to a narrow, black-and-white view of a biological process.  A sort of “Phenoville”.  This was illustrated nicely Read More

CRISPR/Cas9 Screening – The “Copy-Number Effect”

CRISPR/Cas9 Screening – The “Copy-Number Effect”

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Several CRISPR/Cas9 screens identifying essential genes in cancer cell lines have been performed to date (Shalem et al., 2014, Hart et al., 2015, Kiessling et al., 2016). These typically take the form of pooled screens where sgRNA libraries targeting all genes or subsets of genes are introduced in parallel into Cas9-expressing cells, at a single sgRNA per cell. The sgRNAs exert a negative or positive selection pressure on cells based on their impact on cell viability and proliferation. The most Read More

siRNA vs shRNA – applications and off-targeting

siRNA vs shRNA – applications and off-targeting

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Short interfering RNA (siRNA) and short hairpin RNA (shRNA) are both used in RNAi-mediated gene silencing. In this blogpost, we explore the differences in applications of siRNA and shRNA and compare their capacity for off-targeting. For a summary of their properties, please refer to Table 1 at the end of  the post. In what situations should we use siRNA or shRNA? In terms of application, siRNAs are commonly applied for rapid and transient knockdown of gene expression. It is performed in Read More

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