The CRISPR gene editing tool has revolutionized not only the study of genetics and genomics, but the wider field of microbiology as well. Groundbreaking work is continually being done and the recent work by researchers at the New York Genome Center adds to this bank of discoveries. They have developed new CRISPR technology that utilizes a newly discovered enzyme to target and isolate RNA molecules from humans. This is a vital new function that can enable researchers to take a deeper look at genes and isolate genetic data from organic life such as viruses.
Viruses are peculiar organisms that have continued to challenge our assumptions of what it means to be alive. They behave like living organisms but have strange characteristics, one notable one being that they lack DNA and are exclusively made of RNA.
CRISPR is a tool that was created using the Cas9 gene, which is naturally found in bacteria. This gene behaves like a pair of scissors that is guided to a section of DNA which it cuts and extracts. Until now, this tool could only extract DNA molecules, but thanks to this new discovery, RNA molecules can now be targeted. DNA is responsible for storing and transferring the genetic information in an organism. RNA on the other hand is a functional molecule that is used to make amino acids, which are molecules that come together to form proteins.
Recently, a new enzyme called Cas13 has been discovered to target RNA instead of DNA. Cas13 has been proven to allow extraction of RNA without a negative effect to the overall genome which makes its use in potential therapeutic treatment more significant. In addition. Cas13 has also been used to detect the RNA of viruses.
Using Cas 13, the researchers targeted 24,460 different RNA sites in humans and used their data to create a machine learning-based predictive model that hosts a growing library of information. This model can be used to predict the most effective guide for Cas13 to extract custom RNA targets. A random forest pathway, where there are procedural decision trees that the model takes at random and uses the data to classify the identity of the RNA, was found to be the most effective. The model can also be used to identify the degree of genetic instability that would be caused by the extraction of specific RNA molecules.
Another important finding was the discovery of a “seed” region in the RNA. This area is the most effective site to identify an RNA molecule and is a sensitive location that reacts strongly to genetic changes by changing the structure and function of RNA molecules. Identifying the seed region can allow researchers to create guides that can better direct Cas13 to significant portions of RNA.
This model has a plethora of gene editing capabilities. By identifying regions in an RNA molecule that vary in their functional importance, researchers can now make controlled changes to these molecules whilst maintaining their overall integrity and viability. On the other hand, by targeting crucial seed regions, researchers can destabilize and perhaps even destroy specific RNA based organisms such as viruses.
Viruses are made of RNA exclusively and lack DNA, which is why previous CRISPR tools were not useful in studying them. This new CRISPR tool that is specifically made to target RNA now has the potential to be used to treat viruses, which is a claim that the researchers have acknowledged. This can prove to be an invaluable tool that researchers can use to tackle the COVID-19 coronavirus epidemic that is currently affecting the global population. Not only can this model help us develop a solution for COVID-19, it can also help us prevent and understand future viral outbreaks.
Wessels, H., Méndez-Mancilla, A., Guo, X. et al. 2020. Massively parallel Cas13 screens reveal principles for guide RNA design. Nature Biotechnology.