Can we use what we learned from RNAi to guide our use of CRISPR-Cas9 technology?

Learn the key similarities and differences in design and application

Understanding gene function through classical genetics

A little over a 150 years ago, Friar Gregor Mendel began to cross-breed his peas and establish the first rules of heredity. Now we know the traits he followed were encoded by genes within genomic DNA, and the early principles of classical genetics that were developed so long ago (relative to molecular biology) are just as valid and vibrant today. To truly understand the function of a gene, it helps to manipulate the expression of that gene in a living biological system. 

Today, we have several tools to help us manipulate gene expression. To increase gene expression, we have copy DNA (cDNA) and open reading frames (ORFs) which are copies of genes that can be used to supplement expression. To reduce expression, we have a large collection of RNA Interference (RNAi) tools such as short interfering RNA (siRNA), short hairpin RNA (shRNA) and reagents that mimic or inhibit endogenous microRNA.

A new tool for classical genetics

The recent discovery that the elements of a system for bacterial immunity can be re-purposed for use in a variety of genetic applications in mammalian systems has sent waves of excitement through research communities. The elements of this system distill to RNA molecules that can be designed to guide a bacterial nuclease to a very specific target within a genome to carry out a double-strand DNA break that can result in the silencing of that gene. This technique is commonly referred to collectively as a CRISPR-Cas9 gene “knockout”.

“Should I use RNAi or CRISPR-Cas9?”

With any radically new technology, an effort is made to understand how it fits with preceding approaches – and this is especially true of the use of CRISPR-Cas9 in classical genetics experiments. Because both techniques can reduce or effectively silence gene expression, RNAi and CRISPR-Cas9 systems at first seem to be overlapping technologies, but there is much more to the story.

In this Nucleic Acids Research (NAR) publication, Rodolphe Barrangou and his co-authors examine the relationship between RNAi and CRISPR-Cas9 for classical genetics. They examine questions of:

  • efficiency – implications for design
  • specificity and off-target effects
  • role of chemical modifications
  • use as screening tools
  • approaches for analysis of screens
  • in vivo studies

Finally, the authors explore fundamental mechanistic differences and how they can affect interpretation of data between RNAi and CRISPR-Cas9 experiments.

This publication shifts the conversation from "Should I use RNAi or CRISPR-Cas9?" to "I can use both RNAi and CRISPR-Cas9 as complementary tools for more powerful results than ever before!"

Read the full publication

Advances in CRISPR-Cas9 genome engineering: lessons learned from RNA interference »

Additional Information

CRISPR-Cas9 Gene Editing

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RNA Interference

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