Study paves the way towards a more precise use of CRISPR
The results of a Danish research study may be the key to a more effective use of the revolutionary gene technology CRISPR.
Human imagination is the only limit when it comes to the potential of genetic engineering – especially after the breakthrough of CRISPR technology.
A new Danish research project can help refine the method and is a step towards a more precise and effective use of ‘genetic scissors’.
"Our study shows that, by better understanding the CRISPR/Cas9 protein and its gRNA component, we can more accurately hit and cut the DNA and thereby optimise the effectiveness of gene modification," says Yonglun Luo, associate professor at the Department of Biomedicine, Aarhus University.
Ten years ago, researchers identified a protein in bacteria that can cut DNA, and which uses a so-called guide RNA to recognise where DNA needs to be cut. The CRISPR method has been hailed as a revolution within gene technology ever since.
CRISPR makes it possible to remove or insert the exact genes you want in any living organism – from bacteria to plants to humans.
The CRISPR technology also makes it possible to cure diseases through the precise correction of errors appeared in our genes.
This means that the technology has an almost infinite amount of uses within basic research, public health, agriculture and medicine.
Preventing unintended modifications
Implementation of the technology will require that the method is effective and precise, so we only achieve the desired, rather than unintended, gene modifications.
To better understand the mechanisms that affect the effectiveness of the CRISPR method, researchers from the University of Copenhagen and Aarhus University have used an energy-based model to identify the mechanisms regulating CRISPR-Cas9's activity and specification.
This model makes it possible for researchers to design gRNA components that can increase the effectiveness of the method and minimise unintended effects – also known as 'off-target effects'.
"Unintended off-targets are a major concern when using the CRISPR method to treat diseases, and most of the tools for measuring off-targets have serious limitations and do not include the factors that we have discovered in our study. These discoveries have given us the key to designing CRISPR-gRNA with high effectiveness and precision," explains Yonglun Luo.
Refining the method
The researchers behind the study will continue refining the method and the design of the gRNA component to further improve the method's effectiveness and precision.
"We’ll also try to find new methods of measuring on-target and off-target areas and developing innovative methods to address the off-target challenges that still limit our ability to use the CRISPR-Cas9 method," says Yonglun Luo.
The research results - more information
Facts about the type of study: Computational and experimental analysis of CRISPR gene editing activities. The computational study uses an energy-based model for CRISPR-gRNA-target binding to systematically analyse the relationship between nucleotides binding and the CRISPR editing activity on a large dataset of 11062 experimentally validated gRNA efficiencies. The discovery that CRISPR-Cas9 can finetune its binding at the target site by sliding towards overlapping protospacer adjacent motifs (PAMs) to maximize editing efficiency was further validated by measuring SpCas9 cleavage efficiency at 1024 sites using a new library-based method developed by the team.
Partners: The study was conducted in collaboration with Professor Jan Gorodkin’s group at Center for non-coding RNA in Technology and Health, Department of Veterinary and Animal Sciences, University of Copenhagen. Other partners include the Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao; Department of Biology, University of Copenhagen; Division of Oncogenomics, The Netherlands Cancer Institute; and Steno Diabetes Center Aarhus, Aarhus University Hospital.
External funding: Innovation Fund Denmark, Independent Research Fund Denmark, Novo Nordisk Foundation, and European Union’s Horizon 2020 research and innovation programme
Read more: Read the scientific article here: https://www.nature.com/articles/s41467-022-30515-0