The CRISPR-Cas9 system is a tool for cutting DNA at a specifically targeted location. The technique has already revolutionized gene editing but scientists are always looking for new possibilities, so what else can CRISPR do? Since being discovered in a bacterial immune system CRISPR-Cas9 has been adapted into a powerful tool for genomic research. There are two components to the system: a DNA-cutting protein called Cas9 and an RNA molecule known as the guide RNA. Bound together, they form a complex that can identify and cut specific sections of DNA. First, Cas9 has to locate and bind to a common sequence in the genome called a PAM. Once the PAM is bound, the guide RNA unwinds part of the double helix. The RNA strand is designed to match and bind a particular sequence in the DNA. Once it’s found the correct sequence, Cas9 can cut the DNA – its two nuclease domains each make a nick leading to a double strand break. Although the cell will try to repair this break, the fixing process is error-prone and often inadvertently introduces mutations that disable the gene. This makes CRISPR a great tool for knocking out specific genes. But making double strand breaks isn’t all CRISPR can do. Some researchers are deactivating one or both of Cas9’s cutting domains and fusing new enzymes onto the protein. Cas9 can then be used to transport those enzymes to a specific DNA sequence. In one example, Cas9 is fused to an enzyme, a deaminase, which mutates specific DNA bases – eventually replacing cytidine with thymidine. This kind of precise gene editing means you could turn a disease-causing mutation into a healthy version of the gene or introduce a stop codon at a specific place. But it’s not all about gene editing. Several labs have been working on ways to use CRISPR to promote gene transcription. They do this by deactivating Cas9 completely so it can no longer cut DNA. Instead, transcriptional activators are added to the Cas9 by either fusing them directly or via a string of peptides. Alternatively, the activators can be recruited to the guide RNA instead. These activators recruit the cell’s transcription machinery, bringing RNA polymerase and other factors to the target and increasing transcription of that gene. The same principle applies to gene silencing. A KRAB domain fused to the Cas9 inactivates transcription by recruiting more factors that physically block the gene. A more outside-the-box idea for using CRISPR is to attach fluorescent proteins to the complex so you can see where particular DNA sequences are found in the cell. This could be useful for things like visualizing the 3D architecture of the genome, or to paint an entire chromosome and follow its position in the nucleus. CRISPR has already changed the face of research but these new ideas show that what’s been achieved so far could just be the tip of the iceberg when it comes to CRISPR’s potential. Whatever comes next, it seems the CRISPR revolution is far from over.