New CRISPR tool opens up more of the genome for editing

New CRISPR tool opens up more of the genome for editing

 The researchers (left to right) Joseph Jacobson, Pranam Chatterjee, and Noah Jakimo at the MIT Media Lab ©Melanie Gonick
 To carry out the search, the researchers developed a data analysis software tool, which they called SPAMALOT (Search for PAMs by Alignment of Targets). This revealed a number of interesting possible enzymes, but no clear winner. So the team then built synthetic versions of the CRISPRs in the laboratory, to evaluate their performance. They found that the most successful enzyme, a Cas9 from Streptococcus canis (ScCas9), was strikingly similar to the Cas9 enzyme already widely used, according to co-lead author Pranam Chatterjee, a graduate student in the Media Lab, who carried out the research alongside fellow graduate student Noah Jakimo. “The enzyme looks almost identical to the one that was originally discovered … but it is able to target DNA sequences that the commonly used enzyme cannot,” Chatterjee says.

Rather than two G nucleotides as its PAM sequence, the new enzyme needs just one G, opening up far more locations on the genome. This should allow CRISPR to target many disease-specific mutations that have previously been out of reach of the system. For example, a typical gene is around 1,000 bases in length, giving researchers a number of different locations to target if their aim is to simply knock out the entire gene, Jacobson says. However, many diseases, such as sickle cell anemia, are caused by the mutation of a single base, making them much more difficult to target.

“Base editing is not just a matter of hitting that gene anywhere over the 1,000 bases and knocking it out; it is a matter of going in and correcting, in a very precise way, that one base that you want to change, Jacobson says. You need to be able to go to that very exact location, put your piece of CRISPR machinery right next to it, and then with a base editor — another protein that’s attached to the CRISPR — go in and repair or change the base.”The new CRISPR tool could be particularly helpful in such applications. The researchers are now hoping to use their technique to find other enzymes that could expand the targeting range of the CRISPR system even further, without reducing its accuracy.

These findings have been reported in Science Advances.