Choosing the Right Tool for the Job: RNAi, TALEN, or CRISPR

Abstract

The most widely used approach for defining gene function is to reduce or completely disrupt its normal expression. For over a decade, RNAi has ruled the lab, offering a magic bullet to disrupt gene expression in many organisms. However, new biotechnological tools--specifically CRISPR-based technologies--have become available and are squeezing out RNAi dominance in mammalian cell studies. These seemingly competing technologies leave research investigators with the question: "Which technology should I use in my experiment?" This review offers a practical resource to compare and contrast these technologies, guiding the investigator when and where to use this fantastic array of powerful tools.

FIGURE 1. Mechanisms of action of RNAi and TALE/N

(A) RNA interference degrades transcripts post-transcriptionally in the cytoplasm. (B) TALE repression prevents transcription when targeted to the TSS. (C) Dimerized TALENs induce a site specific DSB which is repaired via error-prone NHEJ, potentially leading to frameshift mutations when exons are targeted.

FIGURE 2. Mechanisms of action of CRISPR-based technologies

(A) Cas9 nuclease monomer is guided to its target site via sgRNA and induces site specific DSB which is repaired via error-prone NHEJ, potentially leading to frameshift mutations when exons are targeted. (B) CRISPR interference (CRISPRi) prevents transcription when targeted to the TSS. (C) CRISPR activation (CRISPRa) activates transcription when targeted to the TSS.

FIGURE 3. User guide decision tree for help to choose the right tool

(1) Known sequence. For your targeted organism, what type of known sequence information is available? Transcriptome sequence alone allows the targeting of mRNA (si/shRNAs) and DNA exons (TALENs and Cas9 nuclease). If your organisms’ genome has been sequenced and TSSs have been annotated, all technologies become available, since TALE-repression and CRISPRi/a target promoter regions. (2) Loss-of-function-phenotype. What type of loss-of-function phenotype do you want? While RNAi, TALE-repression, and CRISPRi induce reversible gene knockdown, TALEN and Cas9 nuclease induce a permanent knockout. (3) Time to phenotype. How long will it take from the initial planning of the experiment to finally having a loss-of-function phenotype in cells? Transfection of siRNAs remains the most direct and quickest route. For RNAi using shRNAs as well as CRISPRi/a and Cas9 nuclease, appropriate shRNA/sgRNA plasmids need to be cloned. Moreover, it may be necessary to validate the functionality of Cas9 in target cells. The most time consuming way to induce loss-of-function are TALENs, since each target site requires the design of a specific amino acid sequence of the TALEN DNA binding domain. (4) Type of phenotype. RNAi, TALE-repression and CRISPRi/a are best suited to generate hypomorphic phenotypes that mimic for instance the inhibition of a target by a drug. TALEN and Cas9 nuclease on the other hand can generate complete knockout phenotypes (null allele) via genome editing. (5) Cost of experiment. How much will the production of required reagents cost? shRNAs and sgRNAs are generated by simple cloning or they can be purchased. Because TALEN-based technologies require a more complicated synthesis, cloning them or purchasing them generally costs more. Performing RNAi via siRNAs requires the costly synthesis of short RNAs. (6) Ease of experiment. How much relative effort does it take until one arrives at the desired loss-of-function phenotype? RNAi via siRNAs necessitates only the purchase or synthesis of short RNAs, followed by a simple transfection into target cells. RNAi via shRNAs and CRISPR-based approaches additionally involve the cloning of shRNAs or sgRNAs. The design and cloning of TALEN-based technologies are relatively more complicated, making it less easy to use. (7) Off-targeting. How severe are the known off-target effects? So far, the described off-target effects for CRISPR as well as TALEN technology appear to be less of an issue compared to RNAi. While off-targeting of an si/shRNA to a given RNA can result in an undesired phenotype, it seems likely that TALEN and CRISPR off-targeting to the genomic DNA may not often produce an undesired phenotype.