Researchers discover mechanism disrupting CRISPR-Cas9 gene editing

December 5, 2018, Delft University of Technology
Credit: CC0 Public Domain

The discovery of CRISPR-Cas9 has made gene editing very easy. Unfortunately, the molecular tool has recently been found to be less precise than previously assumed. It can lead to unwanted mutations in a cell's DNA. Researchers at Delft University of Technology have now identified a mechanism that causes such mutations when CRISPR-Cas9 is used incorrectly. This can cause dormant genes to become expressed, which is potentially very dangerous. The researchers have created a checklist based on their findings. Using this checklist will prevent the harmful mechanism from being activated and makes gene editing using CRISPR-Cas9 safer.

Like those of many organisms, contain two copies of each chromosome: one from each parent. These chromosome copies are almost identical, but they contain small differences in a number of . The small variations lead to the genetic differences between individuals. Having a backup for every chromosome may sound like a good thing. However, researchers of Delft University of Technology have found that it can cause problems in combination with the gene editing tool CRISPR-Cas9. "When CRISPR-Cas9 is used to target a single chromosome in heterozygous organisms such as humans, a natural repair mechanism is activated.", said researcher Dr. Jean-Marc Daran. "It turns out that this mechanism uses the other copy of the chromosome as a template for repairing its DNA."

Genome editing

Normally, gene editing experts using CRISPR-Cas9 can change part of the genome of a cell by introducing a new sequence of DNA. The Cas protein cuts open the DNA at a targeted spot, after which the cell is expected to repair its DNA using this new string of genetic material. Thus, new genes can be introduced. "Of course, when the repair mechanism uses the other chromosome as a template instead of the newly introduced string of DNA, the editing will not be successful", said Daran. Since repair using the other chromosome is far more efficient, repair using the intended DNA fragment almost never occurs. Worse than that, loss of heterozygosity can occur, which can have serious health consequences. Diseased genes that were dormant may become expressed, for instance genes that can cause cancer.

Accidental discovery

This discovery of the repair mechanism that blocks gene editing was accidental, as is often the case in science. Arthur Gorter de Vries, a Ph.D. candidate at Delft University of Technology, was working on research involving brewer's yeast. He tried to determine how domestication of brewer's yeast ultimately led to the modern strains of yeast that beer producers now use. "I was trying to remove a certain gene in order to determine its function.", Gorter de Vries said. "Strangely, I could not confirm that I had successfully removed the gene. I also noticed that the cells were behaving erratically." Gorter de Vries was targeting only one of the in his yeast. Further experiments proved that the yeast cells were using the other copy of the targeted chromosome as a template to the DNA that he had been trying to remove.

Harmful mutations

While this newly discovered can prevent gene editing from being successful and can even lead to harmful mutations, this only happens in organism that are heterozygous. "More importantly, the only becomes active if just one chromosome is targeted for editing and not both", said Daran. There are some other factors that need to be taken into account, which is why the researchers have created guidelines to safely edit DNA in heterozygous organisms. The results of their research, including the guidelines, have been published in Nucleic Acids Research.

Explore further: Largest study of CRISPR-Cas9 mutations creates prediction tool for gene editing

More information: Allele-specific genome editing using CRISPR–Cas9 is associated with loss of heterozygosity in diploid yeast. Nucleic Acids Res., DOI: 10.1093/nar/gky1216

Related Stories

A way to detect likelihood of off-target cuts in CRISPR-Cas9

September 13, 2018

An international team of researchers has developed a way to detect the likelihood of making off-target cuts when using the CRISPR-Cas9 gene editing technique. In their paper published in the journal Nature, the group describes ...

Recommended for you

Archaeologists discover Incan tomb in Peru

February 16, 2019

Peruvian archaeologists discovered an Incan tomb in the north of the country where an elite member of the pre-Columbian empire was buried, one of the investigators announced Friday.

Where is the universe hiding its missing mass?

February 15, 2019

Astronomers have spent decades looking for something that sounds like it would be hard to miss: about a third of the "normal" matter in the Universe. New results from NASA's Chandra X-ray Observatory may have helped them ...

What rising seas mean for local economies

February 15, 2019

Impacts from climate change are not always easy to see. But for many local businesses in coastal communities across the United States, the evidence is right outside their doors—or in their parking lots.

The friendly extortioner takes it all

February 15, 2019

Cooperating with other people makes many things easier. However, competition is also a characteristic aspect of our society. In their struggle for contracts and positions, people have to be more successful than their competitors ...


Please sign in to add a comment. Registration is free, and takes less than a minute. Read more

Click here to reset your password.
Sign in to get notified via email when new comments are made.