Bacterial RNA-editing tool could disable viruses or halt disease

Move over DNA, its RNA’s time to shine. A revolutionary RNA-editing tool promises to transform our understanding of RNA’s role in our growth and development, and provide a new avenue for treating infectious diseases and cancer.

RNA was once thought to be a mere middleman, carrying genetic messages from the DNA in the nucleus out to cellular structures called ribosomes, where it directs the production of proteins. In recent decades we have learned that it does much more, from controlling what form a protein will take to influencing whether a particular gene is able to generate a protein.

In other words, although we might think that we are governed by our DNA, it is really RNA that pulls the strings. So people are understandably keen to develop tools to study, track and even manipulate RNA inside living cells.

Genetic warfare

In 2013, a team led by Feng Zhang at the Broad Institute of MIT and Harvard – and another team working independently – figured out how to manipulate a genetic bacterial immune system that can identify and attack an invading pathogen by snipping up sections of its DNA. This CRISPR-Cas system from the bacterium Streptococcus pyogenes is now being used to target and cut up DNA sequences – including those in human cells.

Now Zhang’s team has discovered another version of the CRISPR-Cas system in a bacterium called Leptotrichia shahii. Only this one, called C2c2, selectively cuts up RNA.

To show its promise, Zhang’s team inserted C2c2 into E. coli bacteria, where it silenced a gene by cutting up a form of RNA that carries the gene’s information to the ribosomes.

Silencing genes with C2c2 could make pathogens harmless, says John Rossi at City of Hope medical centre in Duarte, California, who is leading efforts to use RNA molecular tools to fight HIV.

Binding appeal

C2c2 should be able to do more than silence genes. It can also be modified so it binds to RNA but doesn’t cut it up, says Zhang. This means that it could conceivably form part of an editing system to tag RNA so that its movement in the cell can be tracked. This would allow us to alter RNA in a living system and track what effect those alterations are having on the cell or animal as a whole.

“RNA is the blueprint through which genes regulate cellular processes,” says Oliver Rackham at the University of Western Australia. “The exciting thing about this study is that it now opens up the RNA world to the ease of experimental design afforded by CRISPR.”

Rackham is interested in how using C2c2 to target a specific E. coli RNA led to “collateral damage” – RNAs that looked a little like the target molecule were attacked too. Although it might be useful to reduce that collateral damage for some applications, he says it could prove beneficial in others – in a cancer treatment, for example, wiping out “bystander” RNA as well as target RNA might offer a more effective way to fight a tumour.

The tool shop

There is such a hunger for RNA tools that earlier this year, Gene Yeo at the University of California, San Diego, and Jennifer Doudna at the University of California, Berkeley, used some hefty synthetic modifications on the existing CRISPR-Cas system to make it target RNA rather than DNA.

Doudna and Yeo’s tool can already track RNA in mammalian cells, whereas the C2c2 system has so far only been tested in bacteria. But Zhang is confident that with further development C2c2 will be able to bind to mammalian RNAs without cleaving them too.

Both RNA editing tools will be useful, but C2c2 might be more versatile because it is based on a natural RNA targeting system rather than an engineered one.

One thing is clear, says Yeo. “This is the decade where RNA rears its head as being very important for understanding cellular behaviour and disease.”