An Efficient Single-Nucleotide-Editing CRISPR

Comparison of the most used CRISPR system (top) vs. the newly developed editing tool (bottom). In some cases, the difference of just one nucleotide can bring serious disease consequences. Scientists hope to cure such diseases by substituting the incorrect nucleotide with the correct one. [IBS]

Since the discovery of the genome-editing tool CRISPR/Cas9, scientists have been looking to utilize the technology to make a significant impact on correcting genetic diseases. Technical challenges have made it difficult to use this method to correct disorders that are caused by single-nucleotide mutations, such as cystic fibrosis, sickle cell anemia, Huntington's disease, and phenylketonuria. However now, researchers from the Center for Genome Engineering, within the Institute for Basic Science (IBS) in Korea, have just used a variation of CRISPR/Cas9 to produce mice with single-nucleotide differences. The findings from this new study were published recently in Nature Biotechnology in an article entitled “Highly Efficient RNA-Guided Base Editing in Mouse Embryos.”

“Although genome editing with programmable nucleases such as CRISPR–Cas9 or Cpf1 systems holds promise for gene correction to repair genetic defects that cause genetic diseases, it is technically challenging to induce single-nucleotide substitutions in a targeted manner,” the authors wrote. “This is because most DNA double-strand breaks (DSBs) produced by programmable nucleases are repaired by error-prone non-homologous end-joining (NHEJ) rather than homologous recombination (HR) using a template donor DNA. As a result, insertion/deletions (indels) are obtained much more frequently at a nuclease target site than are single-nucleotide substitutions.”

The most frequently used CRISPR/Cas9 technique works by cutting around the faulty nucleotide in both strands of the DNA and cuts out a small part of DNA. In the current study, the investigators used a variation of the Cas9 protein (nickase Cas9, or nCas9) fused with an enzyme called cytidine deaminase, which can substitute one nucleotide into another—generating single-nucleotide substitutions without DNA deletions.

Example of how the IBS scientists created the single-nucleotide substituted mice using the new CRISPR system. [IBS]

The IBS researchers were able to show the efficiency of the CRISPR–nCas9–cytidine deaminase fusion by generating mice that had changes to a single nucleotide in the dystrophin gene (Dmd) or the tyrosinase gene (Tyr). The research team provided evidence that embryos with the single-nucleotide mutation in the Dmd gene led to mice producing no dystrophin protein in their muscles; mice with the Tyr mutation showed albino traits. Mutations in the dystrophin are associated with muscular dystrophy, and tyrosinase controls the production of the skin pigment melanin. Moreover, these single-nucleotide substitutions appeared only in the target position. These results are important because they show that only the correct nucleotide was substituted.        

“We showed here for the first time that programmable deaminases efficiently induced base substitutions in animal embryos, producing mutant mice with disease phenotypes,” remarked senior study investigator Jin-Soo Kim, Ph.D., director of the Center for Genome Engineering at IBS. “This is a proof-of-principle experiment. The next goal is to correct a genetic defect in animals. Ultimately, this technique may allow gene correction in human embryos.”