CRISPR can now target RNA - including coronavirus genome

A new CRISPR-based technology can target RNA in human cells, including the RNA-based genome of the coronavirus. 

Until now all CRISPR approaches have targeted DNA. Using a recently characterised CRISPR-associated enzyme called Cas13, which targets RNA instead of DNA, research groups in the New York Genome Centre and New York University have developed a novel editing tool that can target messenger RNA (mRNA).

The approach could be used to make changes to a cell's gene expression without altering the genome, sidestepping risks associated with off-target effects of genome editing. However mRNAs are also an integral part of how viruses highjack the body's own machinery to reproduce, and the authors hope this approach could be used in the RNA-based genomes of these retroviruses such as the novel coronavirus (SARS-CoV-2).

'We anticipate that RNA-targeting Cas13 enzymes will have a large impact on molecular biology and medical applications, yet little is known about guide RNA design for high targeting efficacy. We set about to change that through an in-depth and systematic study to develop key principles and predictive modelling for most effective guide design' said Dr Neville Sanjana, senior author of the paper, which was published in Nature Biotechnology.

The researchers conducted a screen analysis, testing the gene knock-down efficiency of more than 24,000 Cas13 guide RNA sequences against mammalian mRNA codes. When genes are 'knocked down' they are deactivated or suppressed, rather than deleted completely. Through this testing the team created a machine learning-based predictive model, which can identify the most effective Cas13 guide RNAs.

The team also altered each of the Cas13 guide RNA codes they were testing, making them more or less well-matched to the target mRNA. This led to the identification of a critical 'seed' region of RNA required for specific binding and action of Cas13. This discovery could help reduce off-target activity, which is vital if CRISPR-Cas13 is to be used therapeutically.

Using their model, the researchers have gone on to identify optimal guide RNAs that could be used for future detection and therapeutic targeting of SARS-CoV-2, the virus that causes COVID-19. The Cas13 guide RNAs for a strain of SARS-CoV-2 isolated in New York have been made available online.