Small protein allows for more precise genome editing

Genome editing using small protein structures has the potential to be more efficient, with increased specificity, than current methods – such as CRISPR/Cas genome editing.

While CRISPR/Cas methods have revolutionised work in genetics and genomics, these methods are sometimes limited by the large size of Cas proteins. Researchers at the University of Zürich, Switzerland, and ETH Zürich used a small protein called TnpB, an evolutionary precursor to the Cas12 protein, to improve genome editing efficiency.

'By engineering the small but powerful protein TnpB, we were able to design a variant that shows a 4.4-fold increase in efficiency of modifying DNA – making it more effective as a gene editing tool' said Dr Gerald Schwank from the University of Zurich, who headed the study.

CRISPR/Cas systems have become widespread tools for altering gene sequences and require two parts – a guide RNA sequence which specifies where the alteration should take place, and a Cas protein which induces the required breaks in the DNA sequence.

Cas proteins were found to have evolved from smaller TnpB proteins, which are produced in a range of bacteria that can survive extremely harsh conditions such as acid and severe cold. The researchers hypothesised that, given the shared evolutionary origins of TnpB and Cas proteins, TnpB could act as a smaller pair of 'genetic scissors', allowing easier cell transport and more precise engineering.

However, TnpB had previously been shown to not achieve the same editing efficiency as Cas proteins. Therefore, using a combination of genetic engineering and artificial intelligence, the researchers optimised TnpB for mammalian DNA editing.

'The trick was to modify the tool in two ways: first, so that it more efficiently goes to the nucleus where the genomic DNA is located, and second, so that it also targets alternative genome sequences' said Kim Marquart, PhD student at the University of Zürich and first author of the study published in Nature Methods.

While the study primarily presented the TnpB-based technique as a research resource, improved genome editing approaches may also soon be a significant clinical tool. Focusing on mouse livers, the researchers were able to alter a gene linked with high cholesterol, which is associated with increased risk of heart disease.

'We were able to edit a gene that regulates cholesterol levels, thereby reducing the cholesterol in treated mice by nearly 80 percent,' said Dr Schwank. 'The goal is to develop similar gene editing strategies in humans in order to treat patients suffering from hypercholesterolemia.'