Battle de suprême: CRISPR vs. RNAi based screening


By An Uncharacterized ORF


(Commentators speech log)

Dear XXs and XYs, Welcome to the LoF Screening Championship hosted by the World Federation for Functional Genomics (WFFG). We’re having a gloriously sunny day and a more perfect stage couldn’t be asked for an ultimate entertaining extravaganza. LoF, sounds eerily like ‘laugh' so you may think that this is a competition for the king of comedy of sorts, the one who can leave you Laughing-on-Floor, but sadly it stands for Loss-of-Function.

Loss-of-function screens are concerned with understanding the function of genes by quintessentially removing them from a cell and observing the consequences. For instance, it has been applied in identifying genes that are essential for survival of cancer cells, with the intention to pick out diagnostic markers and targets for drugs, giving them the ability to kill cancer cells. Similar to other functional genomic tools like transcriptome and proteome profiling, LoF screens have also been adapted to high-throughput settings. By nullifying the function of many genes in one go, these techniques can produce a copious amount of data leaving the analyst melancholically overwhelmed.

Today on stage, we have two contestants both of whom have been adapted for high-throughput LoF screens. While one works by knocking down the mRNAs to suppress gene expression, the other works by knocking the gene out. On this sombre thought of gene annihilation, let’s watch this crown battle for the favourite toolkit of natural philosophers, aka scientists.

But first, here’s a quick look at their bios.



Popularly known as RNAi, Ribonucleic Acid interference is the veteran here. Make no mistake, despite the nominal reference to a recreational drug, RNAi’s character remains unblemished by any doping scandals, and most likely is a scornful quip on the scandalous.

Brought out from obscurity by Andrew Fire and Craig Mello in 1998, RNAi generated a huge fire, ahem, fan following and swiftly became the poster child of the Silencer movement that rose to its prominence post-millennium. The arrival of RNAi to the scene provided immense psychological boost to her fans, who could then use it to write their own stories of explorations on suppressing their favourite genes. No wonder RNAi became a heartthrob; for it empowered the people for targeted gene suppression and gave rise to a democratic wave of explorations.

RNAi’s prime strengths are its dicing and slicing abilities that it derives from the adventuring Argonautes. RNAi’s two avatars, siRNA and shRNA, have been successfully deployed by her fans for quite some time. However, as they grew familiar with the technique, RNAi has fallen prey to the old maxim, “familiarity breeds contempt”. Sufficient time has already been devoted to expose RNAi’s shortcomings, inefficient knockdown and off-target effects, that has MELLO-wed the FIRE in RNAi. 



on the other side is a new kid on the block. Clustered Regularly Interspaced Short Palindromic Repeats (catches breath) under the nom de guerre CRISPR has ascended to stellar heights within a very short term. Legend has it that, when CRISPR was young and still hadn’t realised his full potential, he was found protecting bacteria in yogurt from viruses. It was Emanuelle Charpentier, Jennifer Doudna and Feng Zhang who trained CRISPR and helped unleash his capabilities.

CRISPR’s strengths come from its Cas9 arm with which it can break DNA at any address directed by the Guide RNA. CRISPR has become a sensational star and has found a cult fan following in the Genome Editors. Ever since CRISPR came into the scene, the Genome Editing community has been very gung-ho about it, almost to the level that their infectious enthusiasm has raised eyebrows of the Human Germline Ethical Brigade. 

Like RNAi, CRISPR has also been morphed to perform high-throughput LoF screens. The question remains, who is better at it? Let’s hope we will get the answer today.


… Continued … 

Loss-of-Function, Techniques, Comparison, Gene silencing, Genome editing
Last updated: 05.10.2016 - 13:56


Alok Jaiswal
FIMM-EMBL Doctoral Student